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When running SelectVariants with the excludeNonVariants option, remove alleles from the ALT field that are no longer polymorphic.

This commit is contained in:
Eric Banks 2012-04-20 14:30:04 -04:00
parent 79272c5e15
commit f1c5510ec0
2 changed files with 27 additions and 11 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -189,7 +189,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
* or the sample is called reference in this track.
*/
@Input(fullName="discordance", shortName = "disc", doc="Output variants that were not called in this comparison track", required=false)
private RodBinding<VariantContext> discordanceTrack;
protected RodBinding<VariantContext> discordanceTrack;
/**
* A site is considered concordant if (1) we are not looking for specific samples and there is a variant called
@ -197,7 +197,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
* concordance track and they have the sample genotype call.
*/
@Input(fullName="concordance", shortName = "conc", doc="Output variants that were also called in this comparison track", required=false)
private RodBinding<VariantContext> concordanceTrack;
protected RodBinding<VariantContext> concordanceTrack;
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;
@ -230,10 +230,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
public ArrayList<String> SELECT_EXPRESSIONS = new ArrayList<String>();
@Argument(fullName="excludeNonVariants", shortName="env", doc="Don't include loci found to be non-variant after the subsetting procedure", required=false)
private boolean EXCLUDE_NON_VARIANTS = false;
protected boolean EXCLUDE_NON_VARIANTS = false;
@Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci in the analysis", required=false)
private boolean EXCLUDE_FILTERED = false;
protected boolean EXCLUDE_FILTERED = false;
/**
@ -257,23 +257,23 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private Boolean MENDELIAN_VIOLATIONS = false;
@Argument(fullName="mendelianViolationQualThreshold", shortName="mvq", doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation", required=false)
private double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 0;
protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 0;
/**
* Variants are kept in memory to guarantee that exactly n variants will be chosen randomly, so make sure you supply the program with enough memory
* given your input set. This option will NOT work well for large callsets; use --select_random_fraction for sets with a large numbers of variants.
*/
@Argument(fullName="select_random_number", shortName="number", doc="Selects a number of variants at random from the variant track", required=false)
private int numRandom = 0;
protected int numRandom = 0;
/**
* This routine is based on probability, so the final result is not guaranteed to carry the exact fraction. Can be used for large fractions.
*/
@Argument(fullName="select_random_fraction", shortName="fraction", doc="Selects a fraction (a number between 0 and 1) of the total variants at random from the variant track", required=false)
private double fractionRandom = 0;
protected double fractionRandom = 0;
@Argument(fullName="remove_fraction_genotypes", shortName="fractionGenotypes", doc="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall", required=false)
private double fractionGenotypes = 0;
protected double fractionGenotypes = 0;
/**
* This argument select particular kinds of variants out of a list. If left empty, there is no type selection and all variant types are considered for other selection criteria.
@ -508,7 +508,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
if (!selectedTypes.contains(vc.getType()))
continue;
VariantContext sub = subsetRecord(vc, samples);
VariantContext sub = subsetRecord(vc, samples, EXCLUDE_NON_VARIANTS);
if ( (sub.isPolymorphicInSamples() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {
boolean failedJexlMatch = false;
for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
@ -645,11 +645,15 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
* @param samples the samples to extract
* @return the subsetted VariantContext
*/
private VariantContext subsetRecord(VariantContext vc, Set<String> samples) {
private VariantContext subsetRecord(final VariantContext vc, final Set<String> samples, final boolean excludeNonVariants) {
if ( samples == null || samples.isEmpty() )
return vc;
final VariantContext sub = vc.subContextFromSamples(samples, vc.getAlleles());
final VariantContext sub;
if ( excludeNonVariants )
sub = vc.subContextFromSamples(samples); // strip out the alternate alleles that aren't being used
else
sub = vc.subContextFromSamples(samples, vc.getAlleles());
VariantContextBuilder builder = new VariantContextBuilder(sub);
GenotypesContext newGC = sub.getGenotypes();

12
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -163,4 +163,16 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testParallelization (4 threads)--" + testfile, spec);
}
@Test
public void testSelectFromMultiAllelic() {
String testfile = validationDataLocation + "multi-allelic.bi-allelicInGIH.vcf";
String samplesFile = validationDataLocation + "GIH.samples.list";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " -o %s -NO_HEADER -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
1,
Arrays.asList("3fb50cc1c955491048108956d7087c35")
);
executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
}
}