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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
This commit is contained in:
asivache 2009-07-02 20:38:10 +00:00
parent 62807139fc
commit d603145cb0
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -40,10 +40,11 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
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<Integer,Integer> {
* @return
*/
private boolean isCall(Pair<IndelVariant,Integer> 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;