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Oops. Let's make sure only to write calls that the pool supports to the auxiliary vcf files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1974 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-11-04 17:14:55 +00:00
parent 43c3ee61d5
commit eca0942644
1 changed files with 6 additions and 5 deletions
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11
python/expandedSummaryToVCF.py
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@ -145,10 +145,11 @@ for line in callFile:
except KeyError:
# do nothing
pass
#print this out to the file
chromsplit = chrompos.split(":")
outstr=chromsplit[0]+"\t"+chromsplit[1]+"\t"+dbSNP+"\t"+ref+"\t"+variant+"\t"+str(qual)+"\t0\t"+"DP="+str(depth)+";SB="+str(slod)+"\n"
pooledOutputFiles[i].write(outstr)
if grep(poolInternalIDs[i],supportingPools):
#print this out to the file
chromsplit = chrompos.split(":")
outstr=chromsplit[0]+"\t"+chromsplit[1]+"\t"+dbSNP+"\t"+ref+"\t"+variant+"\t"+str(qual)+"\t0\t"+"DP="+str(depth)+";SB="+str(slod)+"\n"
pooledOutputFiles[i].write(outstr)
#now update data
total_slod = total_slod + float(slod)
total_depth = total_depth + int(depth)
@ -163,7 +164,7 @@ for line in callFile:
#propagate individual pool information
for i in range(len(poolNames)):
phase = "0/0"
if grep(poolNames[i],supportingPools):
if grep(poolInternalIDs[i],supportingPools):
phase = "0/1"
else:
phase = "0/0"