Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
This commit is contained in:
Eric Banks
parent
cafc245a43
commit
19e27d4568
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@ -75,9 +75,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
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* -T ReadBackedPhasing
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* -R reference.fasta
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* -I reads.bam
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* --variant:vcf SNPs.vcf
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* -BTI variant
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* -BTIMR INTERSECTION
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* --variant SNPs.vcf
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* -L SNPs.vcf
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* -o phased_SNPs.vcf
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* --phaseQualityThresh 20.0
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* </pre>
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@ -141,7 +141,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
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* <h3>Additional Details</h3>
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* <ul>
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* <li>
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* You should always use -BTI on your VCF track, so that the GATK only looks at the sites on the VCF file.
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* You should always use -L on your VCF track, so that the GATK only looks at the sites on the VCF file.
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* This speeds up the process a lot.
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* </li>
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* <li>
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@ -164,7 +164,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
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* -R human_g1k_v37.fasta
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* -I myNewTechReads.bam
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* -alleles handAnnotatedVCF.vcf
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* -BTI alleles
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* -L handAnnotatedVCF.vcf
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* </pre>
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*
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* <li>
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@ -178,7 +178,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
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* -R human_g1k_v37.fasta
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* -I myTruthDataset.bam
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* -alleles callsToValidate.vcf
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* -BTI alleles
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* -L callsToValidate.vcf
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* -bt
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* -o gav.vcf
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* </pre>
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@ -80,7 +80,7 @@ import java.util.List;
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* -jar GenomeAnalysisTK.jar
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* -T ValidationAmplicons
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* -R /humgen/1kg/reference/human_g1k_v37.fasta
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* -BTI ProbeIntervals
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* -L:table interval_table.table
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* -ProbeIntervals:table interval_table.table
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* -ValidateAlleles:vcf sites_to_validate.vcf
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* -MaskAlleles:vcf mask_sites.vcf
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@ -196,7 +196,7 @@ public class IntervalUtils {
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//if we have an empty list, throw an exception. If they specified intersection and there are no items, this is bad.
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if (retList.size() == 0)
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throw new UserException.BadInput("The INTERSECTION of your -BTI and -L options produced no intervals.");
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throw new UserException.BadInput("The INTERSECTION of your -L options produced no intervals.");
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// we don't need to add the rest of remaining locations, since we know they don't overlap. return what we have
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return retList;
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@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testOverwritingHeader() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
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baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
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Arrays.asList("78d2c19f8107d865970dbaf3e12edd92"));
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executeTest("test overwriting header", spec);
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}
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@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testNoReads() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
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baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
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executeTest("not passing it any reads", spec);
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}
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@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testDBTagWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --dbsnp " + b36dbSNP129 + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
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baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
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executeTest("getting DB tag with dbSNP", spec);
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}
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@ -111,7 +111,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testDBTagWithHapMap() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
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baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
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executeTest("getting DB tag with HM3", spec);
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}
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@ -119,7 +119,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testUsingExpression() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
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baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
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executeTest("using expression", spec);
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}
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@ -129,7 +129,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
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for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + file + " -BTI variant -NO_HEADER", 1,
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baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf -NO_HEADER", 1,
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Arrays.asList(MD5));
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executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
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}
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@ -44,7 +44,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
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@Test
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public void testKnownsOnly() {
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WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
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"-T RealignerTargetCreator -R " + b36KGReference + " --known " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI known -o %s",
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"-T RealignerTargetCreator -R " + b36KGReference + " --known " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s",
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1,
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Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96"));
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executeTest("test rods only", spec3);
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@ -20,7 +20,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
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String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
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String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
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String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
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testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
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testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
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testArgs += " --virtualPrimerSize 30";
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WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
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Arrays.asList("27f9450afa132888a8994167f0035fd7"));
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@ -33,7 +33,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
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String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
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String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
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String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
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testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
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testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
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testArgs += " --virtualPrimerSize 30 --doNotUseBWA";
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WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
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Arrays.asList("f2611ff1d9cd5bedaad003251fed8bc1"));
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@ -46,7 +46,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
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String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
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String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
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String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
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testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
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testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
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testArgs += " --virtualPrimerSize 30 --filterMonomorphic";
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WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
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Arrays.asList("77b3f30e38fedad812125bdf6cf3255f"));
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@ -26,7 +26,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV TiTvVariantEvaluator",
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"-noST",
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"-ST FunctionalClass",
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"-BTI eval",
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"-L " + validationDataLocation + "snpEff.AFR.unfiltered.VariantAnnotator.output.vcf",
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"-o %s"
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),
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1,
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@ -46,7 +46,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-noEV",
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"-EV TiTvVariantEvaluator",
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"-ST Sample",
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"-BTI eval",
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"-L " + variantEvalTestDataRoot + "/CEU.trio.callsForVE.vcf",
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"-o %s"
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),
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1,
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@ -66,7 +66,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-noEV",
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"-EV CountVariants",
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"-noST",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -87,7 +87,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV CountVariants",
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"-noST",
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"-ST Novelty",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -109,7 +109,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-noST",
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"-ST Novelty",
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"-ST Filter",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -130,7 +130,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV CountVariants",
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"-noST",
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"-ST CpG",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -151,7 +151,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV CountVariants",
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"-noST",
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"-ST FunctionalClass",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -172,7 +172,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV CountVariants",
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"-noST",
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"-ST Degeneracy",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -193,7 +193,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV CountVariants",
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"-noST",
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"-ST Sample",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -216,7 +216,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-ST JexlExpression",
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"-select 'DP < 20'",
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"-selectName DepthSelect",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -241,7 +241,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-selectName DepthLt20",
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"-select 'DP > 20'",
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"-selectName DepthGt20",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -260,7 +260,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-noEV",
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"-EV CountVariants",
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"-noST",
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"-BTI eval",
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"-L " + fundamentalTestVCF,
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"-o %s"
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),
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1,
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@ -371,7 +371,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV CompOverlap",
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"-sn HG00625",
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"-noST",
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"-BTI eval",
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"-L " + fundamentalTestSNPsVCF,
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"-o %s"
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),
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1,
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@ -388,7 +388,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-noEV",
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"-EV CompOverlap",
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"-noST",
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"-BTI eval",
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"-L " + fundamentalTestSNPsOneSampleVCF,
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"-o %s"
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),
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1,
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@ -410,7 +410,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-EV CountVariants",
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"-noST",
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"-ST AlleleCount",
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"-BTI eval",
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"-L " + fundamentalTestSNPsVCF,
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"-o %s"
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),
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1,
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@ -17,7 +17,7 @@ public class VCFIntegrationTest extends WalkerTest {
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String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
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String test1 = baseCommand + "-T VariantAnnotator --variant " + testVCF + " -BTI variant";
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String test1 = baseCommand + "-T VariantAnnotator --variant " + testVCF + " -L " + testVCF;
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WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
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List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();
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