Adding docs from Andrey since his repo was all screwed up.
This commit is contained in:
Eric Banks
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@ -68,26 +68,59 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.*;
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import java.util.*;
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/**
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* Tool for calling indels in Tumor-Normal paired sample mode; this tool supports single-sample mode as well,
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* but this latter functionality is now superceded by UnifiedGenotyper.
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*
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* <p>
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* This is a simple, counts-and-cutoffs based tool for calling indels from aligned (preferrably MSA cleaned) sequencing
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* data. Two output formats supported are: BED format (minimal output, required), and extended output that includes read
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* and mismtach statistics around the calls (tuned on with --verbose). The calls can be performed from a single/pooled sample,
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* or from a matched pair of samples (with --somatic option). In the latter case, two input bam files must be specified,
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* the order is important: indels are called from the second sample ("Tumor") and additionally annotated as germline
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* if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic
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* if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
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* only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
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* data. Supported output formats are: BED format, extended verbose output (tab separated), and VCF. The latter two outputs
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* include additional statistics such as mismtaches and base qualitites around the calls, read strandness (how many
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* forward/reverse reads support ref and indel alleles) etc. It is highly recommended to use these additional
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* statistics to perform post-filtering of the calls as the tool is tuned for sensitivity (in other words it will
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* attempt to "call" anything remotely reasonable based only on read counts and will generate all the additional
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* metrics for the post-processing tools to make the final decision). The calls are performed by default
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* from a matched tumor-normal pair of samples. In this case, two (sets of) input bam files must be specified using tagged -I
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* command line arguments: normal and tumor bam(s) must be passed with -I:normal and -I:tumor arguments,
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* respectively. Indels are called from the tumor sample and annotated as germline
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* if even a weak evidence for the same indel, not necessarily a confident call, exists in the normal sample, or as somatic
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* if normal sample has coverage at the site but no indication for an indel. Note that strictly speaking the calling
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* is not even attempted in normal sample: if there is an indel in normal that is not detected/does not pass a threshold
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* in tumor sample, it will not be reported.
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*
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* <b>If any of the general usage of this tool or any of the command-line arguments for this tool are not clear to you,
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* please email asivache at broadinstitute dot org and he will gladly explain everything in more detail.</b>
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* To make indel calls and associated metrics for a single sample, this tool can be run with --unpaired flag (input
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* bam tagging is not required in this case, and tags are completely ignored if still used: all input bams will be merged
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* on the fly and assumed to represent a single sample - this tool does not check for sample id in the read groups).
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*
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* <h2>Input</h2>
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* <p>
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* Tumor and normal bam files (or single sample bam file(s) in --unpaired mode).
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* </p>
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*
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* <h2>Output</h2>
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* <p>
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* Indel calls with associated metrics.
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* </p>
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*
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* <h2>Examples</h2>
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* <pre>
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* java -Xmx2g -jar GenomeAnalysisTK.jar \
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* -R ref.fasta \
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* -T SomaticIndelDetector \
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* -o indels.vcf \
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* -verbose indels.txt
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* -I:normal normal.bam \
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* -I:tumor tumor.bam
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* </pre>
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*
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*/
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@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
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public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
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// @Output
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// PrintStream out;
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@Output(doc="File to which variants should be written",required=true)
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@Output(doc="File to write variants (indels) in VCF format",required=true)
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protected VCFWriter vcf_writer = null;
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@Argument(fullName="outputFile", shortName="O", doc="output file name (BED format). DEPRECATED> Use --bed", required=true)
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@ -102,68 +135,80 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
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@Hidden
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@Argument(fullName = "genotype_intervals", shortName = "genotype",
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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)
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doc = "Calls will be made at each position within the specified interval(s), whether there is an indel or not", required = false)
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public String genotypeIntervalsFile = null;
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@Hidden
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@Argument(fullName="genotypeIntervalsAreNotSorted", shortName="giNotSorted", required=false,
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doc="This tool assumes that the genotyping interval list (--genotype_intervals) is sorted; "+
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"if the list turns out to be unsorted, it will throw an exception. "+
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"Use this argument when your interval list is not sorted to instruct the IndelGenotyper "+
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"to sort and keep it in memory (increases memory usage!).")
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doc="This tool assumes that the genotyping interval list (--genotype_intervals) is sorted; "+
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"if the list turns out to be unsorted, it will throw an exception. "+
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"Use this argument when your interval list is not sorted to instruct the IndelGenotyper "+
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"to sort and keep it in memory (increases memory usage!).")
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protected boolean GENOTYPE_NOT_SORTED = false;
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@Hidden
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@Argument(fullName="unpaired", shortName="unpaired",
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doc="Perform unpaired calls (no somatic status detection)", required=false)
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@Argument(fullName="unpaired", shortName="unpaired",
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doc="Perform unpaired calls (no somatic status detection)", required=false)
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boolean call_unpaired = false;
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boolean call_somatic ;
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boolean call_somatic ;
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@Argument(fullName="verboseOutput", shortName="verbose",
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doc="Verbose output file in text format", required=false)
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java.io.File verboseOutput = null;
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@Argument(fullName="verboseOutput", shortName="verbose",
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doc="Verbose output file in text format", required=false)
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java.io.File verboseOutput = null;
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@Argument(fullName="bedOutput", shortName="bed",
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doc="Lightweight bed output file (only positions and events, no stats/annotations)", required=false)
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doc="Lightweight bed output file (only positions and events, no stats/annotations)", required=false)
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java.io.File bedOutput = null;
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@Argument(fullName="minCoverage", shortName="minCoverage",
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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)
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int minCoverage = 6;
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@Argument(fullName="minCoverage", shortName="minCoverage",
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doc="indel calls will be made only at sites with tumor coverage of minCoverage or more reads; "+
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"with --unpaired (single sample) option, this value is used for minimum sample coverage", required=false)
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int minCoverage = 6;
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@Argument(fullName="minNormalCoverage", shortName="minNormalCoverage",
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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)
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int minNormalCoverage = 4;
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@Argument(fullName="minNormalCoverage", shortName="minNormalCoverage",
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doc="used only in default (somatic) mode; normal sample must have at least minNormalCoverage "+
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"or more reads at the site to call germline/somatic indel, otherwise the indel (in tumor) is ignored", required=false)
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int minNormalCoverage = 4;
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@Argument(fullName="minFraction", shortName="minFraction",
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doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for making a call"+
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" (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false)
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double minFraction = 0.3;
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@Argument(fullName="minFraction", shortName="minFraction",
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doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for making a call"+
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" (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false)
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double minFraction = 0.3;
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@Argument(fullName="minConsensusFraction", shortName="minConsensusFraction",
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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)
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double minConsensusFraction = 0.7;
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@Argument(fullName="minConsensusFraction", shortName="minConsensusFraction",
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doc="Indel call is made only if fraction of CONSENSUS indel observations at a site wrt "+
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"all indel observations at the site exceeds this threshold", required=false)
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double minConsensusFraction = 0.7;
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@Argument(fullName="minIndelCount", shortName="minCnt",
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doc="Minimum count of reads supporting consensus indel required for making the call. "+
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" This filter supercedes minFraction, i.e. indels with acceptable minFraction at low coverage "+
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"(minIndelCount not met) will not pass.", required=false)
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int minIndelCount = 0;
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@Argument(fullName="minIndelCount", shortName="minCnt",
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doc="Minimum count of reads supporting consensus indel required for making the call. "+
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" This filter supercedes minFraction, i.e. indels with acceptable minFraction at low coverage "+
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"(minIndelCount not met) will not pass.", required=false)
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int minIndelCount = 0;
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@Argument(fullName="refseq", shortName="refseq",
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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)
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String RefseqFileName = null;
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@Argument(fullName="refseq", shortName="refseq",
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doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with "+
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"GENOMIC/UTR/INTRON/CODING and with the gene name", required=false)
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String RefseqFileName = null;
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@Argument(fullName="blacklistedLanes", shortName="BL",
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doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+
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"by this application, so they will not contribute indels to consider and will not be counted.", required=false)
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PlatformUnitFilterHelper dummy;
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@Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging, do not turn this on",required=false) Boolean DEBUG = false;
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//@Argument(fullName="blacklistedLanes", shortName="BL",
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// doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+
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// "by this application, so they will not contribute indels to consider and will not be counted.", required=false)
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//PlatformUnitFilterHelper dummy;
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@Hidden
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@Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging, do not turn this on",
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required=false) Boolean DEBUG = false;
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@Argument(fullName="window_size", shortName="ws", doc="Size (bp) of the sliding window used for accumulating the coverage. "+
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"May need to be increased to accomodate longer reads or longer deletions.",required=false) int WINDOW_SIZE = 200;
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"May need to be increased to accomodate longer reads or longer deletions. A read can be fit into the "+
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"window if its length on the reference (i.e. read length + length of deletion gap(s) if any) is smaller "+
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"than the window size. Reads that do not fit will be ignored, so long deletions can not be called "+
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"if window is too small",required=false) int WINDOW_SIZE = 200;
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@Argument(fullName="maxNumberOfReads",shortName="mnr",doc="Maximum number of reads to cache in the window; if number of reads exceeds this number,"+
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" the window will be skipped and no calls will be made from it",required=false) int MAX_READ_NUMBER = 10000;
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private WindowContext tumor_context;
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private WindowContext normal_context;
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private int currentContigIndex = -1;
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