From 1e682deb26aad12d4421cf9ff7f08318c1cd4ab3 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Thu, 15 Sep 2011 13:07:50 -0400 Subject: [PATCH 01/14] Minor html-formatting-related documentation fix to the SnpEff class. --- .../org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index 14abbca5b..bb3685fb5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -45,7 +45,7 @@ import java.util.*; * (http://snpeff.sourceforge.net/). * * For each variant, chooses one of the effects of highest biological impact from the SnpEff - * output file (which must be provided on the command line via --snpEffFile .vcf), + * output file (which must be provided on the command line via --snpEffFile filename.vcf), * and adds annotations on that effect. * * @author David Roazen From 202405b1a165db3f1d97f687da10826df181c849 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 13:52:31 -0400 Subject: [PATCH 02/14] Updating the FunctionalClass stratification in VariantEval to handle the snpEff annotations; this change really needs to be in before the release so that the pipeline can output semi-meaningful plots. This commit maintains backwards compatibility with the crappy Genomic Annotator output. However, I did clean up the code a bit so that we now use an Enum instead of hard-coded values (so it's now much easier to change things if we choose to do so in the future). I do not see this as the final commit on this topic - I think we need to make some changes to the snpEff annotator to preferentially choose certain annotations within effect classes; Mark, let's chat about this for a bit when you get back next week. Also, for the record, I should be blamed for David's temporary commit the other day because I gave him the green light (since when do you care about backwards compatibility anyways?). In any case, at least now we have something that works for both the old and new annotations. --- .../stratifications/FunctionalClass.java | 53 +++++++++++++------ .../VariantEvalIntegrationTest.java | 25 ++++++++- 2 files changed, 59 insertions(+), 19 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index 193a65591..a32857ffc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; @@ -11,12 +12,19 @@ import java.util.List; * Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation. */ public class FunctionalClass extends VariantStratifier { + + public enum FunctionalType { + silent, + missense, + nonsense + } + + @Override public void initialize() { states.add("all"); - states.add("silent"); - states.add("missense"); - states.add("nonsense"); + for ( FunctionalType type : FunctionalType.values() ) + states.add(type.name()); } @@ -26,10 +34,12 @@ public class FunctionalClass extends VariantStratifier { relevantStates.add("all"); if (eval != null && eval.isVariant()) { - String type = null; + FunctionalType type = null; if (eval.hasAttribute("refseq.functionalClass")) { - type = eval.getAttributeAsString("refseq.functionalClass"); + try { + type = FunctionalType.valueOf(eval.getAttributeAsString("refseq.functionalClass")); + } catch ( Exception e ) {} // don't error out if the type isn't supported } else if (eval.hasAttribute("refseq.functionalClass_1")) { int annotationId = 1; String key; @@ -37,24 +47,33 @@ public class FunctionalClass extends VariantStratifier { do { key = String.format("refseq.functionalClass_%d", annotationId); - String newtype = eval.getAttributeAsString(key); - - if ( newtype != null && !newtype.equalsIgnoreCase("null") && - ( type == null || - ( type.equals("silent") && !newtype.equals("silent") ) || - ( type.equals("missense") && newtype.equals("nonsense") ) ) - ) { - type = newtype; + String newtypeStr = eval.getAttributeAsString(key); + if ( newtypeStr != null && !newtypeStr.equalsIgnoreCase("null") ) { + try { + FunctionalType newType = FunctionalType.valueOf(newtypeStr); + if ( type == null || + ( type == FunctionalType.silent && newType != FunctionalType.silent ) || + ( type == FunctionalType.missense && newType == FunctionalType.nonsense ) ) { + type = newType; + } + } catch ( Exception e ) {} // don't error out if the type isn't supported } annotationId++; } while (eval.hasAttribute(key)); + + } else if ( eval.hasAttribute(SnpEff.InfoFieldKey.EFF.name() ) ) { + SnpEff.EffectType snpEffType = SnpEff.EffectType.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.EFF.name()).toString()); + if ( snpEffType == SnpEff.EffectType.STOP_GAINED ) + type = FunctionalType.nonsense; + else if ( snpEffType == SnpEff.EffectType.NON_SYNONYMOUS_CODING ) + type = FunctionalType.missense; + else if ( snpEffType == SnpEff.EffectType.SYNONYMOUS_CODING ) + type = FunctionalType.silent; } - if (type != null) { - if (type.equals("silent")) { relevantStates.add("silent"); } - else if (type.equals("missense")) { relevantStates.add("missense"); } - else if (type.equals("nonsense")) { relevantStates.add("nonsense"); } + if ( type != null ) { + relevantStates.add(type.name()); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index e992684bc..d8f7ad3b6 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -6,7 +6,7 @@ import org.testng.annotations.Test; import java.util.Arrays; public class VariantEvalIntegrationTest extends WalkerTest { - private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval"; + private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval"; private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf"; private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf"; private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf"; @@ -14,6 +14,27 @@ public class VariantEvalIntegrationTest extends WalkerTest { private static String cmdRoot = "-T VariantEval" + " -R " + b36KGReference; + @Test + public void testFunctionClassWithSnpeff() { + WalkerTestSpec spec = new WalkerTestSpec( + buildCommandLine( + "-T VariantEval", + "-R " + b37KGReference, + "--dbsnp " + b37dbSNP132, + "--eval " + validationDataLocation + "snpEff.AFR.unfiltered.VariantAnnotator.output.vcf", + "-noEV", + "-EV TiTvVariantEvaluator", + "-noST", + "-ST FunctionalClass", + "-BTI eval", + "-o %s" + ), + 1, + Arrays.asList("f5f811ceb973d7fd6c1b2b734f1b2b12") + ); + executeTest("testStratifySamplesAndExcludeMonomorphicSites", spec); + } + @Test public void testStratifySamplesAndExcludeMonomorphicSites() { WalkerTestSpec spec = new WalkerTestSpec( @@ -21,7 +42,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-T VariantEval", "-R " + b37KGReference, "--dbsnp " + b37dbSNP132, - "--eval " + variantEvalTestDataRoot + "/CEU.trio.callsForVE.vcf", + "--eval " + variantEvalTestDataRoot + "CEU.trio.callsForVE.vcf", "-noEV", "-EV TiTvVariantEvaluator", "-ST Sample", From d369d105932b457a01b47166b7b7a1cd41d6b337 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 13:56:23 -0400 Subject: [PATCH 03/14] Adding documentation before the release for GATK wiki page --- .../broadinstitute/sting/gatk/filters/PlatformFilter.java | 2 +- .../sting/gatk/walkers/PrintReadsWalker.java | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java index 30b2f828d..8e241bb2c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java @@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils; * @version 0.1 */ public class PlatformFilter extends ReadFilter { - @Argument(fullName = "PLFilterName", shortName = "PLFilterName", doc="Discard reads with RG:PL attribute containing this strign", required=false) + @Argument(fullName = "PLFilterName", shortName = "PLFilterName", doc="Discard reads with RG:PL attribute containing this string", required=false) protected String[] PLFilterNames; public boolean filterOut(SAMRecord rec) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java index fdfac6bf7..4f072e88c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java @@ -68,6 +68,13 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; * -I input1.bam \ * -I input2.bam \ * --read_filter MappingQualityZero + * + * java -Xmx2g -jar GenomeAnalysisTK.jar \ + * -R ref.fasta \ + * -T PrintReads \ + * -o output.bam \ + * -I input.bam \ + * -n 2000 * * */ From ce73dc40712510a360738df49e802b4c21d95621 Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 15 Sep 2011 15:33:09 -0400 Subject: [PATCH 04/14] Update to the bindings for liftOverVCF.pl (to -V from -B) --- public/perl/liftOverVCF.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/perl/liftOverVCF.pl b/public/perl/liftOverVCF.pl index 21cb8bb6b..ba4198292 100755 --- a/public/perl/liftOverVCF.pl +++ b/public/perl/liftOverVCF.pl @@ -36,7 +36,7 @@ my $unsorted_vcf = "$tmp_prefix.unsorted.vcf"; # lift over the file print "Lifting over the vcf..."; -my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict"; +my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -V:variant $in -o $unsorted_vcf -chain $chain -dict $newRef.dict"; if ($recordOriginalLocation) { $cmd .= " -recordOriginalLocation"; } @@ -66,7 +66,7 @@ system($cmd) == 0 or quit("The sorting step failed. Please correct the necessar # Filter the VCF for bad records print "\nFixing/removing bad records...\n"; -$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $sorted_vcf -o $out"; +$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -V:variant $sorted_vcf -o $out"; system($cmd) == 0 or quit("The filtering step failed. Please correct the necessary errors before retrying."); # clean up From f04e51c6c2b74a79644e9473230410a8ba85fe92 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 15:38:56 -0400 Subject: [PATCH 05/14] Adding docs from Andrey since his repo was all screwed up. --- .../indels/SomaticIndelDetectorWalker.java | 143 ++++++++++++------ 1 file changed, 94 insertions(+), 49 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java index e5ad3106d..8bba8eac2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java @@ -68,26 +68,59 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.*; import java.util.*; + /** + * Tool for calling indels in Tumor-Normal paired sample mode; this tool supports single-sample mode as well, + * but this latter functionality is now superceded by UnifiedGenotyper. + * + *

* This is a simple, counts-and-cutoffs based tool for calling indels from aligned (preferrably MSA cleaned) sequencing - * data. Two output formats supported are: BED format (minimal output, required), and extended output that includes read - * and mismtach statistics around the calls (tuned on with --verbose). The calls can be performed from a single/pooled sample, - * or from a matched pair of samples (with --somatic option). In the latter case, two input bam files must be specified, - * the order is important: indels are called from the second sample ("Tumor") and additionally annotated as germline - * if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic - * if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains - * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords. + * data. Supported output formats are: BED format, extended verbose output (tab separated), and VCF. The latter two outputs + * include additional statistics such as mismtaches and base qualitites around the calls, read strandness (how many + * forward/reverse reads support ref and indel alleles) etc. It is highly recommended to use these additional + * statistics to perform post-filtering of the calls as the tool is tuned for sensitivity (in other words it will + * attempt to "call" anything remotely reasonable based only on read counts and will generate all the additional + * metrics for the post-processing tools to make the final decision). The calls are performed by default + * from a matched tumor-normal pair of samples. In this case, two (sets of) input bam files must be specified using tagged -I + * command line arguments: normal and tumor bam(s) must be passed with -I:normal and -I:tumor arguments, + * respectively. Indels are called from the tumor sample and annotated as germline + * if even a weak evidence for the same indel, not necessarily a confident call, exists in the normal sample, or as somatic + * if normal sample has coverage at the site but no indication for an indel. Note that strictly speaking the calling + * is not even attempted in normal sample: if there is an indel in normal that is not detected/does not pass a threshold + * in tumor sample, it will not be reported. * - * If any of the general usage of this tool or any of the command-line arguments for this tool are not clear to you, - * please email asivache at broadinstitute dot org and he will gladly explain everything in more detail. + * To make indel calls and associated metrics for a single sample, this tool can be run with --unpaired flag (input + * bam tagging is not required in this case, and tags are completely ignored if still used: all input bams will be merged + * on the fly and assumed to represent a single sample - this tool does not check for sample id in the read groups). * + *

Input

+ *

+ * Tumor and normal bam files (or single sample bam file(s) in --unpaired mode). + *

+ * + *

Output

+ *

+ * Indel calls with associated metrics. + *

+ * + *

Examples

+ * 
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T SomaticIndelDetector \
+ *   -o indels.vcf \
+ *   -verbose indels.txt
+ *   -I:normal normal.bam \
+ *   -I:tumor tumor.bam
+ *
* */ + @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class}) public class SomaticIndelDetectorWalker extends ReadWalker { // @Output // PrintStream out; - @Output(doc="File to which variants should be written",required=true) + @Output(doc="File to write variants (indels) in VCF format",required=true) protected VCFWriter vcf_writer = null; @Argument(fullName="outputFile", shortName="O", doc="output file name (BED format). DEPRECATED> Use --bed", required=true) @@ -102,68 +135,80 @@ public class SomaticIndelDetectorWalker extends ReadWalker { @Hidden @Argument(fullName = "genotype_intervals", shortName = "genotype", - doc = "Calls will be made at each position within the specified interval(s), whether there is an indel or it's the ref", required = false) + doc = "Calls will be made at each position within the specified interval(s), whether there is an indel or not", required = false) public String genotypeIntervalsFile = null; @Hidden @Argument(fullName="genotypeIntervalsAreNotSorted", shortName="giNotSorted", required=false, - doc="This tool assumes that the genotyping interval list (--genotype_intervals) is sorted; "+ - "if the list turns out to be unsorted, it will throw an exception. "+ - "Use this argument when your interval list is not sorted to instruct the IndelGenotyper "+ - "to sort and keep it in memory (increases memory usage!).") + doc="This tool assumes that the genotyping interval list (--genotype_intervals) is sorted; "+ + "if the list turns out to be unsorted, it will throw an exception. "+ + "Use this argument when your interval list is not sorted to instruct the IndelGenotyper "+ + "to sort and keep it in memory (increases memory usage!).") protected boolean GENOTYPE_NOT_SORTED = false; @Hidden - @Argument(fullName="unpaired", shortName="unpaired", - doc="Perform unpaired calls (no somatic status detection)", required=false) + @Argument(fullName="unpaired", shortName="unpaired", + doc="Perform unpaired calls (no somatic status detection)", required=false) boolean call_unpaired = false; - boolean call_somatic ; + boolean call_somatic ; - @Argument(fullName="verboseOutput", shortName="verbose", - doc="Verbose output file in text format", required=false) - java.io.File verboseOutput = null; + @Argument(fullName="verboseOutput", shortName="verbose", + doc="Verbose output file in text format", required=false) + java.io.File verboseOutput = null; @Argument(fullName="bedOutput", shortName="bed", - doc="Lightweight bed output file (only positions and events, no stats/annotations)", required=false) + doc="Lightweight bed output file (only positions and events, no stats/annotations)", required=false) java.io.File bedOutput = null; - @Argument(fullName="minCoverage", shortName="minCoverage", - doc="indel calls will be made only at sites with coverage of minCoverage or more reads; with --somatic this value is applied to tumor sample", required=false) - int minCoverage = 6; + @Argument(fullName="minCoverage", shortName="minCoverage", + doc="indel calls will be made only at sites with tumor coverage of minCoverage or more reads; "+ + "with --unpaired (single sample) option, this value is used for minimum sample coverage", required=false) + int minCoverage = 6; - @Argument(fullName="minNormalCoverage", shortName="minNormalCoverage", - doc="used only with --somatic; normal sample must have at least minNormalCoverage or more reads at the site to call germline/somatic indel, otherwise the indel (in tumor) is ignored", required=false) - int minNormalCoverage = 4; + @Argument(fullName="minNormalCoverage", shortName="minNormalCoverage", + doc="used only in default (somatic) mode; normal sample must have at least minNormalCoverage "+ + "or more reads at the site to call germline/somatic indel, otherwise the indel (in tumor) is ignored", required=false) + int minNormalCoverage = 4; - @Argument(fullName="minFraction", shortName="minFraction", - doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for making a call"+ - " (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false) - double minFraction = 0.3; + @Argument(fullName="minFraction", shortName="minFraction", + doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for making a call"+ + " (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false) + double minFraction = 0.3; - @Argument(fullName="minConsensusFraction", shortName="minConsensusFraction", - doc="Indel call is made only if fraction of CONSENSUS indel observations at a site wrt all indel observations at the site exceeds this threshold", required=false) - double minConsensusFraction = 0.7; + @Argument(fullName="minConsensusFraction", shortName="minConsensusFraction", + doc="Indel call is made only if fraction of CONSENSUS indel observations at a site wrt "+ + "all indel observations at the site exceeds this threshold", required=false) + double minConsensusFraction = 0.7; - @Argument(fullName="minIndelCount", shortName="minCnt", - doc="Minimum count of reads supporting consensus indel required for making the call. "+ - " This filter supercedes minFraction, i.e. indels with acceptable minFraction at low coverage "+ - "(minIndelCount not met) will not pass.", required=false) - int minIndelCount = 0; + @Argument(fullName="minIndelCount", shortName="minCnt", + doc="Minimum count of reads supporting consensus indel required for making the call. "+ + " This filter supercedes minFraction, i.e. indels with acceptable minFraction at low coverage "+ + "(minIndelCount not met) will not pass.", required=false) + int minIndelCount = 0; - @Argument(fullName="refseq", shortName="refseq", - doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with GENOMIC/UTR/INTRON/CODING and with the gene name", required=false) - String RefseqFileName = null; + @Argument(fullName="refseq", shortName="refseq", + doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with "+ + "GENOMIC/UTR/INTRON/CODING and with the gene name", required=false) + String RefseqFileName = null; - @Argument(fullName="blacklistedLanes", shortName="BL", - doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+ - "by this application, so they will not contribute indels to consider and will not be counted.", required=false) - PlatformUnitFilterHelper dummy; - @Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging, do not turn this on",required=false) Boolean DEBUG = false; +//@Argument(fullName="blacklistedLanes", shortName="BL", +// doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+ +// "by this application, so they will not contribute indels to consider and will not be counted.", required=false) +//PlatformUnitFilterHelper dummy; + + @Hidden + @Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging, do not turn this on", + required=false) Boolean DEBUG = false; @Argument(fullName="window_size", shortName="ws", doc="Size (bp) of the sliding window used for accumulating the coverage. "+ - "May need to be increased to accomodate longer reads or longer deletions.",required=false) int WINDOW_SIZE = 200; + "May need to be increased to accomodate longer reads or longer deletions. A read can be fit into the "+ + "window if its length on the reference (i.e. read length + length of deletion gap(s) if any) is smaller "+ + "than the window size. Reads that do not fit will be ignored, so long deletions can not be called "+ + "if window is too small",required=false) int WINDOW_SIZE = 200; @Argument(fullName="maxNumberOfReads",shortName="mnr",doc="Maximum number of reads to cache in the window; if number of reads exceeds this number,"+ " the window will be skipped and no calls will be made from it",required=false) int MAX_READ_NUMBER = 10000; + + private WindowContext tumor_context; private WindowContext normal_context; private int currentContigIndex = -1; From fe474b77f85f325ed20d6cb6c50dc298d024d03e Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 16:05:39 -0400 Subject: [PATCH 06/14] Updating docs so printing looks nicer --- .../gatk/walkers/variantutils/VariantValidationAssessor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index b98646270..ea8549474 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; /** - * Annotates a validation (from e.g. Sequenom) VCF with QC metrics (HW-equilibrium, % failed probes) + * Annotates a validation (from Sequenom for example) VCF with QC metrics (HW-equilibrium, % failed probes) * *

* The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes). From 4ef6a4598c3704fd5aac5f5302a148ddfedd3958 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 16:10:34 -0400 Subject: [PATCH 07/14] Updating docs to include output --- .../walkers/varianteval/VariantEvalWalker.java | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 266b97af0..28f4f2a56 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -56,6 +56,22 @@ import java.util.*; *

Output

*

* Evaluation tables detailing the results of the eval modules which were applied. + * For example: + * 

+ * output.eval.gatkreport:
+ * ##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample
+ * CountVariants  CompRod   CpG      EvalRod  JexlExpression  Novelty  nProcessedLoci  nCalledLoci  nRefLoci  nVariantLoci  variantRate ...
+ * CountVariants  dbsnp     CpG      eval     none            all      65900028        135770       0         135770        0.00206024  ...
+ * CountVariants  dbsnp     CpG      eval     none            known    65900028        47068        0         47068         0.00071423  ...
+ * CountVariants  dbsnp     CpG      eval     none            novel    65900028        88702        0         88702         0.00134601  ...
+ * CountVariants  dbsnp     all      eval     none            all      65900028        330818       0         330818        0.00502000  ...
+ * CountVariants  dbsnp     all      eval     none            known    65900028        120685       0         120685        0.00183133  ...
+ * CountVariants  dbsnp     all      eval     none            novel    65900028        210133       0         210133        0.00318866  ...
+ * CountVariants  dbsnp     non_CpG  eval     none            all      65900028        195048       0         195048        0.00295976  ...
+ * CountVariants  dbsnp     non_CpG  eval     none            known    65900028        73617        0         73617         0.00111710  ...
+ * CountVariants  dbsnp     non_CpG  eval     none            novel    65900028        121431       0         121431        0.00184265  ...
+ * ...
+ *
*

* *

Examples

From 6d02a34bfba1537f294f5a077b24702e539b87a5 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 16:17:54 -0400 Subject: [PATCH 08/14] Updating docs to include output --- .../variantutils/VariantValidationAssessor.java | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index ea8549474..8eaf976d0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -57,7 +57,16 @@ import java.util.*; * *

Output

*

- * An annotated VCF. + * An annotated VCF. Additionally, a table like the following will be output: + * 

+ *     Total number of samples assayed:                  185
+ *     Total number of records processed:                152
+ *     Number of Hardy-Weinberg violations:              34 (22%)
+ *     Number of no-call violations:                     12 (7%)
+ *     Number of homozygous variant violations:          0 (0%)
+ *     Number of records passing all filters:            106 (69%)
+ *     Number of passing records that are polymorphic:   98 (92%)
+ *
*

* *

Examples

From fd1831b4a520e68b15b6b5b958aa2d04ade4e287 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 16:25:03 -0400 Subject: [PATCH 09/14] Updating docs to include more details --- .../gatk/walkers/fasta/FastaAlternateReferenceWalker.java | 6 ++++-- .../sting/gatk/walkers/fasta/FastaReferenceWalker.java | 3 +++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index fd912334f..4e2c17bf6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -43,8 +43,10 @@ import java.util.List; * Generates an alternative reference sequence over the specified interval. * *

- * Given variant ROD tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). - * Additionally, allows for a "snpmask" ROD to set overlapping bases to 'N'. + * Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). + * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'. + * Note that if there are multiple variants at a site, it takes the first one seen. + * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order). * *

Input

*

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java index 5f3b37cc8..7ae5c5c75 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java @@ -42,6 +42,9 @@ import java.io.PrintStream; * *

* The output format can be partially controlled using the provided command-line arguments. + * Specify intervals with the usual -L argument to output only the reference bases within your intervals. + * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a + * separate fasta sequence (named numerically in order). * *

Input

*

From 2f58fdb369a3cd4857281dd210427fac6352ca88 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 15 Sep 2011 16:26:11 -0400 Subject: [PATCH 10/14] Adding expected output doc to CountCovariates --- .../recalibration/CountCovariatesWalker.java | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java index 98c8950e3..1bdb70bdd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java @@ -76,6 +76,42 @@ import java.util.Map; *

Output

*

* A recalibration table file in CSV format that is used by the TableRecalibration walker. + * It is a comma-separated text file relating the desired covariates to the number of such bases and their rate of mismatch in the genome, and its implied empirical quality score. + * + * The first 20 lines of such a file is shown below. + * * The file begins with a series of comment lines describing: + * ** The number of counted loci + * ** The number of counted bases + * ** The number of skipped loci and the fraction skipped, due to presence in dbSNP or bad reference bases + * + * * After the comments appears a header line indicating which covariates were used as well as the ordering of elements in the subsequent records. + * + * * After the header, data records occur one per line until the end of the file. The first several items on a line are the values of the individual covariates and will change + * depending on which covariates were specified at runtime. The last three items are the data- that is, number of observations for this combination of covariates, number of + * reference mismatches, and the raw empirical quality score calculated by phred-scaling the mismatch rate. + * + * 

+ * # Counted Sites    19451059
+ * # Counted Bases    56582018
+ * # Skipped Sites    82666
+ * # Fraction Skipped 1 / 235 bp
+ * ReadGroup,QualityScore,Cycle,Dinuc,nObservations,nMismatches,Qempirical
+ * SRR006446,11,65,CA,9,1,10
+ * SRR006446,11,48,TA,10,0,40
+ * SRR006446,11,67,AA,27,0,40
+ * SRR006446,11,61,GA,11,1,10
+ * SRR006446,12,34,CA,47,1,17
+ * SRR006446,12,30,GA,52,1,17
+ * SRR006446,12,36,AA,352,1,25
+ * SRR006446,12,17,TA,182,11,12
+ * SRR006446,11,48,TG,2,0,40
+ * SRR006446,11,67,AG,1,0,40
+ * SRR006446,12,34,CG,9,0,40
+ * SRR006446,12,30,GG,43,0,40
+ * ERR001876,4,31,AG,1,0,40
+ * ERR001876,4,31,AT,2,2,1
+ * ERR001876,4,31,CA,1,0,40
+ *
*

* *

Examples

From 9dc6354130b23683c31a7b2c1ef8c2ed94da1946 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 15 Sep 2011 16:55:24 -0400 Subject: [PATCH 11/14] Oops didn't mean to touch this test before --- .../gatk/walkers/varianteval/VariantEvalIntegrationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index d8f7ad3b6..99622cbf6 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -42,7 +42,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-T VariantEval", "-R " + b37KGReference, "--dbsnp " + b37dbSNP132, - "--eval " + variantEvalTestDataRoot + "CEU.trio.callsForVE.vcf", + "--eval " + variantEvalTestDataRoot + "/CEU.trio.callsForVE.vcf", "-noEV", "-EV TiTvVariantEvaluator", "-ST Sample", From d78e00e5b2cd5e8a1b1aa75209100b039e521442 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Thu, 15 Sep 2011 16:09:07 -0400 Subject: [PATCH 12/14] Renaming VariantAnnotator SnpEff keys This is to head off potential confusion with the output from the SnpEff tool itself, which also uses a key named EFF. --- .../sting/gatk/walkers/annotator/SnpEff.java | 90 ++++++++++--------- .../stratifications/FunctionalClass.java | 4 +- .../VariantAnnotatorIntegrationTest.java | 2 +- .../VariantEvalIntegrationTest.java | 2 +- 4 files changed, 53 insertions(+), 45 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index bb3685fb5..4ead77506 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -68,23 +68,31 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio // Key names for the INFO field annotations we will add to each record, along // with parsing-related information: public enum InfoFieldKey { - EFF (-1), - EFF_IMPACT (0), - EFF_CODON_CHANGE (1), - EFF_AMINO_ACID_CHANGE (2), - EFF_GENE_NAME (3), - EFF_GENE_BIOTYPE (4), - EFF_TRANSCRIPT_ID (6), - EFF_EXON_ID (7); + EFFECT_KEY ("SNPEFF_EFFECT", -1), + IMPACT_KEY ("SNPEFF_IMPACT", 0), + CODON_CHANGE_KEY ("SNPEFF_CODON_CHANGE", 1), + AMINO_ACID_CHANGE_KEY ("SNPEFF_AMINO_ACID_CHANGE", 2), + GENE_NAME_KEY ("SNPEFF_GENE_NAME", 3), + GENE_BIOTYPE_KEY ("SNPEFF_GENE_BIOTYPE", 4), + TRANSCRIPT_ID_KEY ("SNPEFF_TRANSCRIPT_ID", 6), + EXON_ID_KEY ("SNPEFF_EXON_ID", 7); + + // Actual text of the key + private final String keyName; // Index within the effect metadata subfields from the SnpEff EFF annotation // where each key's associated value can be found during parsing. private final int fieldIndex; - InfoFieldKey ( int fieldIndex ) { + InfoFieldKey ( String keyName, int fieldIndex ) { + this.keyName = keyName; this.fieldIndex = fieldIndex; } + public String getKeyName() { + return keyName; + } + public int getFieldIndex() { return fieldIndex; } @@ -292,27 +300,27 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio } public List getKeyNames() { - return Arrays.asList( InfoFieldKey.EFF.toString(), - InfoFieldKey.EFF_IMPACT.toString(), - InfoFieldKey.EFF_CODON_CHANGE.toString(), - InfoFieldKey.EFF_AMINO_ACID_CHANGE.toString(), - InfoFieldKey.EFF_GENE_NAME.toString(), - InfoFieldKey.EFF_GENE_BIOTYPE.toString(), - InfoFieldKey.EFF_TRANSCRIPT_ID.toString(), - InfoFieldKey.EFF_EXON_ID.toString() + return Arrays.asList( InfoFieldKey.EFFECT_KEY.getKeyName(), + InfoFieldKey.IMPACT_KEY.getKeyName(), + InfoFieldKey.CODON_CHANGE_KEY.getKeyName(), + InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(), + InfoFieldKey.GENE_NAME_KEY.getKeyName(), + InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), + InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), + InfoFieldKey.EXON_ID_KEY.getKeyName() ); } public List getDescriptions() { return Arrays.asList( - new VCFInfoHeaderLine(InfoFieldKey.EFF.toString(), 1, VCFHeaderLineType.String, "The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)"), - new VCFInfoHeaderLine(InfoFieldKey.EFF_IMPACT.toString(), 1, VCFHeaderLineType.String, "Impact of the highest-impact effect resulting from the current variant " + Arrays.toString(EffectImpact.values())), - new VCFInfoHeaderLine(InfoFieldKey.EFF_CODON_CHANGE.toString(), 1, VCFHeaderLineType.String, "Old/New codon for the highest-impact effect resulting from the current variant"), - new VCFInfoHeaderLine(InfoFieldKey.EFF_AMINO_ACID_CHANGE.toString(), 1, VCFHeaderLineType.String, "Old/New amino acid for the highest-impact effect resulting from the current variant"), - new VCFInfoHeaderLine(InfoFieldKey.EFF_GENE_NAME.toString(), 1, VCFHeaderLineType.String, "Gene name for the highest-impact effect resulting from the current variant"), - new VCFInfoHeaderLine(InfoFieldKey.EFF_GENE_BIOTYPE.toString(), 1, VCFHeaderLineType.String, "Gene biotype for the highest-impact effect resulting from the current variant"), - new VCFInfoHeaderLine(InfoFieldKey.EFF_TRANSCRIPT_ID.toString(), 1, VCFHeaderLineType.String, "Transcript ID for the highest-impact effect resulting from the current variant"), - new VCFInfoHeaderLine(InfoFieldKey.EFF_EXON_ID.toString(), 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant") + new VCFInfoHeaderLine(InfoFieldKey.EFFECT_KEY.getKeyName(), 1, VCFHeaderLineType.String, "The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)"), + new VCFInfoHeaderLine(InfoFieldKey.IMPACT_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Impact of the highest-impact effect resulting from the current variant " + Arrays.toString(EffectImpact.values())), + new VCFInfoHeaderLine(InfoFieldKey.CODON_CHANGE_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Old/New codon for the highest-impact effect resulting from the current variant"), + new VCFInfoHeaderLine(InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Old/New amino acid for the highest-impact effect resulting from the current variant"), + new VCFInfoHeaderLine(InfoFieldKey.GENE_NAME_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Gene name for the highest-impact effect resulting from the current variant"), + new VCFInfoHeaderLine(InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Gene biotype for the highest-impact effect resulting from the current variant"), + new VCFInfoHeaderLine(InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Transcript ID for the highest-impact effect resulting from the current variant"), + new VCFInfoHeaderLine(InfoFieldKey.EXON_ID_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant") ); } @@ -375,16 +383,16 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio } try { - impact = EffectImpact.valueOf(effectMetadata[InfoFieldKey.EFF_IMPACT.getFieldIndex()]); + impact = EffectImpact.valueOf(effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]); } catch ( IllegalArgumentException e ) { - parseError(String.format("Unrecognized value for effect impact: %s", effectMetadata[InfoFieldKey.EFF_IMPACT.getFieldIndex()])); + parseError(String.format("Unrecognized value for effect impact: %s", effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()])); } - codonChange = effectMetadata[InfoFieldKey.EFF_CODON_CHANGE.getFieldIndex()]; - aminoAcidChange = effectMetadata[InfoFieldKey.EFF_AMINO_ACID_CHANGE.getFieldIndex()]; - geneName = effectMetadata[InfoFieldKey.EFF_GENE_NAME.getFieldIndex()]; - geneBiotype = effectMetadata[InfoFieldKey.EFF_GENE_BIOTYPE.getFieldIndex()]; + codonChange = effectMetadata[InfoFieldKey.CODON_CHANGE_KEY.getFieldIndex()]; + aminoAcidChange = effectMetadata[InfoFieldKey.AMINO_ACID_CHANGE_KEY.getFieldIndex()]; + geneName = effectMetadata[InfoFieldKey.GENE_NAME_KEY.getFieldIndex()]; + geneBiotype = effectMetadata[InfoFieldKey.GENE_BIOTYPE_KEY.getFieldIndex()]; if ( effectMetadata[SNPEFF_CODING_FIELD_INDEX].trim().length() > 0 ) { try { @@ -398,8 +406,8 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio coding = EffectCoding.UNKNOWN; } - transcriptID = effectMetadata[InfoFieldKey.EFF_TRANSCRIPT_ID.getFieldIndex()]; - exonID = effectMetadata[InfoFieldKey.EFF_EXON_ID.getFieldIndex()]; + transcriptID = effectMetadata[InfoFieldKey.TRANSCRIPT_ID_KEY.getFieldIndex()]; + exonID = effectMetadata[InfoFieldKey.EXON_ID_KEY.getFieldIndex()]; } private void parseError ( String message ) { @@ -443,14 +451,14 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio public Map getAnnotations() { Map annotations = new LinkedHashMap(Utils.optimumHashSize(InfoFieldKey.values().length)); - addAnnotation(annotations, InfoFieldKey.EFF.toString(), effect.toString()); - addAnnotation(annotations, InfoFieldKey.EFF_IMPACT.toString(), impact.toString()); - addAnnotation(annotations, InfoFieldKey.EFF_CODON_CHANGE.toString(), codonChange); - addAnnotation(annotations, InfoFieldKey.EFF_AMINO_ACID_CHANGE.toString(), aminoAcidChange); - addAnnotation(annotations, InfoFieldKey.EFF_GENE_NAME.toString(), geneName); - addAnnotation(annotations, InfoFieldKey.EFF_GENE_BIOTYPE.toString(), geneBiotype); - addAnnotation(annotations, InfoFieldKey.EFF_TRANSCRIPT_ID.toString(), transcriptID); - addAnnotation(annotations, InfoFieldKey.EFF_EXON_ID.toString(), exonID); + addAnnotation(annotations, InfoFieldKey.EFFECT_KEY.getKeyName(), effect.toString()); + addAnnotation(annotations, InfoFieldKey.IMPACT_KEY.getKeyName(), impact.toString()); + addAnnotation(annotations, InfoFieldKey.CODON_CHANGE_KEY.getKeyName(), codonChange); + addAnnotation(annotations, InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(), aminoAcidChange); + addAnnotation(annotations, InfoFieldKey.GENE_NAME_KEY.getKeyName(), geneName); + addAnnotation(annotations, InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), geneBiotype); + addAnnotation(annotations, InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), transcriptID); + addAnnotation(annotations, InfoFieldKey.EXON_ID_KEY.getKeyName(), exonID); return annotations; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index a32857ffc..88ffcaaeb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -62,8 +62,8 @@ public class FunctionalClass extends VariantStratifier { annotationId++; } while (eval.hasAttribute(key)); - } else if ( eval.hasAttribute(SnpEff.InfoFieldKey.EFF.name() ) ) { - SnpEff.EffectType snpEffType = SnpEff.EffectType.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.EFF.name()).toString()); + } else if ( eval.hasAttribute(SnpEff.InfoFieldKey.EFFECT_KEY.getKeyName() ) ) { + SnpEff.EffectType snpEffType = SnpEff.EffectType.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.EFFECT_KEY.getKeyName()).toString()); if ( snpEffType == SnpEff.EffectType.STOP_GAINED ) type = FunctionalType.nonsense; else if ( snpEffType == SnpEff.EffectType.NON_SYNONYMOUS_CODING ) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index f902ce276..08baae7a7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -134,7 +134,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation + "snpEff.AFR.unfiltered.vcf -L 1:1-1,500,000", 1, - Arrays.asList("a1c3ba9efc28ee0606339604095076ea") + Arrays.asList("486fc6a5ca1819f5ab180d5d72b1ebc9") ); executeTest("Testing SnpEff annotations", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 99622cbf6..b90e6d0ff 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -32,7 +32,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { 1, Arrays.asList("f5f811ceb973d7fd6c1b2b734f1b2b12") ); - executeTest("testStratifySamplesAndExcludeMonomorphicSites", spec); + executeTest("testFunctionClassWithSnpeff", spec); } @Test From 9fdf1f8eb663858cacafd8fb339d098cdce4b96d Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 15 Sep 2011 21:05:22 -0400 Subject: [PATCH 13/14] Fix some doc formatting for Depth of Coverage --- .../gatk/walkers/coverage/DepthOfCoverageWalker.java | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 3a18fe610..86f97a36c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -69,14 +69,23 @@ import java.util.*; *

Output

*

* Tables pertaining to different coverage summaries. Suffix on the table files declares the contents: + *

* - no suffix: per locus coverage + *

* - _summary: total, mean, median, quartiles, and threshold proportions, aggregated over all bases + *

* - _statistics: coverage histograms (# locus with X coverage), aggregated over all bases + *

* - _interval_summary: total, mean, median, quartiles, and threshold proportions, aggregated per interval + *

* - _interval_statistics: 2x2 table of # of intervals covered to >= X depth in >=Y samples + *

* - _gene_summary: total, mean, median, quartiles, and threshold proportions, aggregated per gene + *

* - _gene_statistics: 2x2 table of # of genes covered to >= X depth in >= Y samples + *

* - _cumulative_coverage_counts: coverage histograms (# locus with >= X coverage), aggregated over all bases + *

* - _cumulative_coverage_proportions: proprotions of loci with >= X coverage, aggregated over all bases *

* From 939babc820cc5174a1d97a8b6bdb992ca6cedc09 Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 15 Sep 2011 21:05:51 -0400 Subject: [PATCH 14/14] Updating formating for ValidationAmplicons GATK docs --- .../sting/gatk/walkers/validation/ValidationAmplicons.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 01e8cd321..48cba6a1a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -61,7 +61,7 @@ import java.util.List; * CACGTTCGGcttgtgcagagcctcaaggtcatccagaggtgatAGTTTAGGGCCCTCTCAAGTCTTTCCNGTGCGCATGG[GT/AC*]CAGCCCTGGGCACCTGTNNNNNNNNNNNNNTGCTCATGGCCTTCTAGATTCCCAGGAAATGTCAGAGCTTTTCAAAGCCC * * are amplicon sequences resulting from running the tool. The flags (preceding the sequence itself) can be: - * + *
  * Valid                     // amplicon is valid
  * SITE_IS_FILTERED=1        // validation site is not marked 'PASS' or '.' in its filter field ("you are trying to validate a filtered variant")
  * VARIANT_TOO_NEAR_PROBE=1  // there is a variant too near to the variant to be validated, potentially shifting the mass-spec peak
@@ -72,10 +72,10 @@ import java.util.List;
  * END_TOO_CLOSE,            // variant is too close to the end of the amplicon region to give sequenom a good chance to find a suitable primer
  * NO_VARIANTS_FOUND,        // no variants found within the amplicon region
  * INDEL_OVERLAPS_VALIDATION_SITE, // an insertion or deletion interferes directly with the site to be validated (i.e. insertion directly preceding or postceding, or a deletion that spans the site itself)
- * 

+ *

* *

Examples

- * 

+ * 
  *    java
  *      -jar GenomeAnalysisTK.jar
  *      -T ValidationAmplicons