From d603145cb042f54f11be16039e47cc953303a7ec Mon Sep 17 00:00:00 2001 From: asivache Date: Thu, 2 Jul 2009 20:38:10 +0000 Subject: [PATCH] Meaning of input arguments has CHANGED: minFraction is now a minimum fraction of CONSENSUS indel observation, out of all reads covering the site, required to make the call. minConsensusFraction is still the minimum fraction of CONSENSUS indel observation out of all indel observations at the site git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1160 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/IndelGenotyperWalker.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java index b938aa027..dfa3b039b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java @@ -40,10 +40,11 @@ public class IndelGenotyperWalker extends ReadWalker { doc="used only with --somatic; normal sample must have at least minNormalCoverage or more reads to call germline/somatic indel", required=false) int minNormalCoverage = 4; @Argument(fullName="minFraction", shortName="minFraction", - doc="minimum fraction of reads with indels at a site, out of all reads covering the site, required for a call", required=false) + doc="minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for a consensus call"+ + " (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false) double minFraction = 0.3; @Argument(fullName="minConsensusFraction", shortName="minConsensusFraction", - doc="Minimum fraction of reads with indel at the site that must contain consensus indel in order to make the call", required=false) + doc="Minimum fraction of CONSENSUS indel observations at a site wrt all indel observations at the site required to make the call", required=false) double minConsensusFraction = 0.7; @Argument(fullName="refseq", shortName="refseq", doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated as GENOMIC/UTR/INTRON/CODING", required=false) @@ -299,7 +300,7 @@ public class IndelGenotyperWalker extends ReadWalker { * @return */ private boolean isCall(Pair p, int coverage) { - return ( (double)p.second > minFraction * coverage && (double) p.first.getCount() > minConsensusFraction*p.second ); + return ( (double)p.first.getCount() > minFraction * coverage && (double) p.first.getCount() > minConsensusFraction*p.second ); } /** Build output line for bed file and write it to the specified output writer if the latter is not null;