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Merge pull request #1182 from broadinstitute/rhl_laatv_multiallelic 

Update doc for multiallelics, trimming is the default behavior
This commit is contained in:
Ron Levine 2015-10-22 08:04:34 -04:00
parent 7b067c13bd 795fe75886
commit aa3087c0d1
2 changed files with 99 additions and 34 deletions
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27
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
View File

@ -66,17 +66,36 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
1,
Arrays.asList("dd238fe14b4a495a489907c1e021221e"));
Arrays.asList("5d82f53b036d9a0fca170e5be68d5ab2"));
executeTest("test left alignment", spec);
}
@Test
public void testLeftAlignmentWithTrimmingAndMultialleliecs() {
public void testLeftAlignmentDontTrim() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -trim -split",
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header",
1,
Arrays.asList("dd238fe14b4a495a489907c1e021221e"));
executeTest("test left alignment, don't trim", spec);
}
@Test
public void testLeftAlignmentWithMultialleliecs() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -split",
1,
Arrays.asList("534bea653d4a0e59e74f4107c1768558"));
executeTest("test left alignment with trimming and hard multiple alleles", spec);
executeTest("test left alignment with hard multiple alleles", spec);
}
@Test
public void testLeftAlignmentDontTrimWithMultialleliecs() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header -split",
1,
Arrays.asList("189b8136ee62b54bf7b227e99c892440"));
executeTest("test left alignment with hard multiple alleles, don't trim", spec);
}
}

106
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
View File

@ -60,11 +60,12 @@ import java.util.*;
* Left-align indels in a variant callset
*
* <p>
* LeftAlignAndTrimVariants is a tool that takes a VCF file and left-aligns the indels inside it. The same indel can often be
* placed at multiple positions and still represent the same haplotype. While the standard convention with VCF is to
* place an indel at the left-most position this doesn't always happen, so this tool can be used to left-align them.
* Note that this tool cannot handle anything other than bi-allelic, simple indels. Complex events are written out unchanged.
* Optionally, the tool will also trim common bases from indels, leaving them with a minimum representation.</p>
* LeftAlignAndTrimVariants is a tool that takes a VCF file, left-aligns the indels and trims common bases from indels,
* leaving them with a minimum representation. The same indel can often be placed at multiple positions and still
* represent the same haplotype. While the standard convention with VCF is to place an indel at the left-most position
* this isn't always done, so this tool can be used to left-align them. This tool optionally splits multiallelic
* sites into biallelics and left-aligns individual alleles. Optionally, the tool will not trim common bases from indels.
* </p>
*
* <h3>Input</h3>
* <p>
@ -76,7 +77,9 @@ import java.util.*;
* A left-aligned VCF.
* </p>
*
* <h3>Usage example</h3>
* <h3>Usage examples</h3>
*
* <h4>Left align and trim alleles</h4>
* <pre>
* java -jar GenomeAnalysisTK.jar \
* -T LeftAlignAndTrimVariants \
@ -85,6 +88,37 @@ import java.util.*;
* -o output.vcf
* </pre>
*
* <h4>Left align and don't trim alleles</h4>
* <pre>
* java -jar GenomeAnalysisTK.jar \
* -T LeftAlignAndTrimVariants \
* -R reference.fasta \
* --variant input.vcf \
* -o output.vcf
* --dontTrimAlleles
* </pre>
*
* <h4>Split multiallics into biallelics, left align and trim alleles</h4>
* <pre>
* java -jar GenomeAnalysisTK.jar \
* -T LeftAlignAndTrimVariants \
* -R reference.fasta \
* --variant input.vcf \
* -o output.vcf
* --splitMultiallelics
* </pre>
*
* <h4>Split multiallelics into biallics, left align but don't trim alleles</h4>
* <pre>
* java -jar GenomeAnalysisTK.jar \
* -T LeftAlignAndTrimVariants \
* -R reference.fasta \
* --variant input.vcf \
* -o output.vcf
* --splitMultiallelics
* --dontTrimAlleles
* </pre>
*
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-200,stop=200)) // WARNING: if this changes,MAX_INDEL_LENGTH needs to change as well!
@ -94,10 +128,10 @@ public class LeftAlignAndTrimVariants extends RodWalker<Integer, Integer> {
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
/**
* If this argument is set, bases common to all alleles will be removed, leaving only their minimal representation.
* If this argument is set, bases common to all alleles will not be removed and will not leave their minimal representation.
*/
@Argument(fullName="trimAlleles", shortName="trim", doc="Trim alleles to remove bases common to all of them", required=false)
protected boolean trimAlleles = false;
@Argument(fullName="dontTrimAlleles", shortName="notrim", doc="Do not Trim alleles to remove bases common to all of them", required=false)
protected boolean dontTrimAlleles = false;
/**
* If this argument is set, split multiallelic records and left-align individual alleles.
@ -132,32 +166,16 @@ public class LeftAlignAndTrimVariants extends RodWalker<Integer, Integer> {
int changedSites = 0;
for ( final VariantContext vc : VCs ) {
// split first into biallelics, and optionally trim alleles to minimal representation
Pair<VariantContext,Integer> result = new Pair<VariantContext, Integer>(vc,0); // default value
// split first into biallelics, and optionally don't trim alleles to minimal representation
if (splitMultiallelics) {
final List<VariantContext> vcList = GATKVariantContextUtils.splitVariantContextToBiallelics(vc);
for (final VariantContext biallelicVC: vcList) {
final VariantContext v = (trimAlleles ? GATKVariantContextUtils.trimAlleles(biallelicVC,true,true) : biallelicVC);
result = alignAndWrite(v, ref);
// strip out PLs and AD if we've subsetted the alleles
if ( vcList.size() > 1 )
result.first = new VariantContextBuilder(result.first).genotypes(GATKVariantContextUtils.stripPLsAndAD(result.first.getGenotypes())).make();
writer.add(result.first);
changedSites += result.second;
changedSites += trimAlignWrite(biallelicVC, ref, vcList.size());
}
}
else {
if (trimAlleles)
result = alignAndWrite(GATKVariantContextUtils.trimAlleles(vc,true,true), ref);
else
result = alignAndWrite(vc,ref);
writer.add(result.first);
changedSites += result.second;
changedSites += trimAlignWrite(vc, ref, 1);
}
}
return changedSites;
@ -175,11 +193,39 @@ public class LeftAlignAndTrimVariants extends RodWalker<Integer, Integer> {
}
/**
* Main routine workhorse. By definitio, it will only take biallelic vc's. Splitting into multiple alleles has to be
* Trim, align and write out the vc.
*
* @param vc Input VC with variants to left align
* @param ref Reference context
* @param numBiallelics Number of biallelics from the original VC
* @return Number of records left-aligned (0 or 1)
*/
@Requires("vc != null")
protected int trimAlignWrite(final VariantContext vc, final ReferenceContext ref, final int numBiallelics ){
// optionally don't trim VC
final VariantContext v = dontTrimAlleles ? vc : GATKVariantContextUtils.trimAlleles(vc, true, true);
// align the VC
final Pair<VariantContext,Integer> result = alignAndWrite(v, ref);
// strip out PLs and AD if we've subsetted the alleles
if ( numBiallelics > 1 )
result.first = new VariantContextBuilder(result.first).genotypes(GATKVariantContextUtils.stripPLsAndAD(result.first.getGenotypes())).make();
// write out new VC
writer.add(result.first);
// number of records left aligned
return result.second;
}
/**
* Main routine workhorse. By definition, it will only take biallelic vc's. Splitting into multiple alleles has to be
* handled by calling routine.
* @param vc Input VC with variants to left align
* @param ref Reference context
* @return # of records left-aligned (0 or 1) and new VC.
* @return Number of records left-aligned (0 or 1) and new VC.
*/
@Requires({"vc != null","ref != null", "vc.isBiallelic() == true","ref.getBases().length>=2*MAX_INDEL_LENGTH+1"})
@Ensures({"result != null","result.first != null", "result.second >=0"})