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what used to be internal cutoff values are now exposed as cmdline parameters: minCoverage, minNormalCoverage, minFraction, minConsensusFraction 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@995 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-11 21:22:52 +00:00
parent 41687d5237
commit 4eda040e0f
1 changed files with 17 additions and 7 deletions
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24
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -2,10 +2,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.indels;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet; import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.Set; import java.util.Set;
import net.sf.samtools.Cigar; import net.sf.samtools.Cigar;
@ -31,6 +29,18 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="verbose", shortName="verbose", @Argument(fullName="verbose", shortName="verbose",
doc="Tell us what you are calling now (printed to stdout)", required=false) doc="Tell us what you are calling now (printed to stdout)", required=false)
public boolean verbose = false; public boolean verbose = false;
@Argument(fullName="minCoverage", shortName="minCoverage",
doc="must have minCoverage or more reads to call indel; with --somatic this value is applied to tumor sample", required=false)
public int minCoverage = 6;
@Argument(fullName="minNormalCoverage", shortName="minNormalCoverage",
doc="used only with --somatic; normal sample must have at least minNormalCoverage or more reads to call germline/somatic indel", required=false)
public 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)
public 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)
public double minConsensusFraction = 0.7;
private static int WINDOW_SIZE = 200; private static int WINDOW_SIZE = 200;
private RunningCoverage coverage; private RunningCoverage coverage;
@ -215,7 +225,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
int cov = coverage.coverageAt(pos); int cov = coverage.coverageAt(pos);
if ( cov < 6 ) continue; // low coverage if ( cov < minCoverage ) continue; // low coverage
int total_variant_count = 0; int total_variant_count = 0;
int max_variant_count = 0; int max_variant_count = 0;
@ -231,7 +241,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
event_length = var.lengthOnRef(); event_length = var.lengthOnRef();
} }
} }
if ( (double)total_variant_count > 0.3*cov && (double) max_variant_count > 0.7*total_variant_count ) { if ( (double)total_variant_count > minFraction * cov && (double) max_variant_count > minConsensusFraction*total_variant_count ) {
try { try {
output.write(refName+"\t"+(pos-1)+"\t"+(event_length > 0 ? pos-1+event_length : pos-1)+ output.write(refName+"\t"+(pos-1)+"\t"+(event_length > 0 ? pos-1+event_length : pos-1)+
@ -268,8 +278,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
int tumor_cov = coverage.coverageAt(pos); int tumor_cov = coverage.coverageAt(pos);
int normal_cov = normal_coverage.coverageAt(pos); int normal_cov = normal_coverage.coverageAt(pos);
if ( tumor_cov < 6 ) continue; // low coverage if ( tumor_cov < minCoverage ) continue; // low coverage
if ( normal_cov < 4 ) continue; // low coverage if ( normal_cov < minNormalCoverage ) continue; // low coverage
int total_variant_count_tumor = 0; int total_variant_count_tumor = 0;
int max_variant_count_tumor = 0; int max_variant_count_tumor = 0;
@ -286,7 +296,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} }
} }
if ( (double)total_variant_count_tumor > 0.3*tumor_cov && (double) max_variant_count_tumor > 0.7*total_variant_count_tumor ) { if ( (double)total_variant_count_tumor > minFraction * tumor_cov && (double) max_variant_count_tumor > minConsensusFraction*total_variant_count_tumor ) {
String message = refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+ String message = refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+
"\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov; "\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov;