From 5d85bd9671f27432d76861d72904c6a80a73546c Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 16 Sep 2009 16:46:09 +0000 Subject: [PATCH] By default, VF should ask for deleted bases so that they show up in coverage. The Strand filter then needs to ignore those bases when determining bias. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1636 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/filters/VECFisherStrand.java | 4 ++++ .../gatk/walkers/filters/VariantFiltrationWalker.java | 8 ++++++++ 2 files changed, 12 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java index dd0b74f8d..cbb212ac0 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java @@ -186,6 +186,10 @@ public class VECFisherStrand implements VariantExclusionCriterion { SAMRecord read = reads.get(readIndex); int offset = offsets.get(readIndex); + // skip over deletion sites + if ( offset == -1 ) + continue; + int readAllele = BaseUtils.simpleBaseToBaseIndex(read.getReadString().charAt(offset)); boolean isFW = !read.getReadNegativeStrandFlag(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 250e65cbb..8f93b80e5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -197,6 +197,14 @@ public class VariantFiltrationWalker extends LocusWalker { */ public Integer reduceInit() { return 0; } + + /** + * We want reads that span deletions + * + * @return true + */ + public boolean includeReadsWithDeletionAtLoci() { return true; } + /** * For each site of interest, rescore the genotype likelihoods by applying the specified feature set. *