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Restore "type" annotation (but not genomechange or cDNA change, which are already encoded in the VCF) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3784 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-13 17:33:15 +00:00
parent 9d2a485532
commit 19a5830186
1 changed files with 3 additions and 0 deletions
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3
python/AnnotateVCFwithMAF.py
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@ -77,6 +77,9 @@ def addFormat(infoString):
last = val[len(val)-1]
num = val.split(".")[1][1:len(val.split(".")[1])-1]
newItems.append("proteinchange="+first+">"+last+";proteinoffset="+num)
if key == "type" :
newItems.append(item)
return ";".join(newItems)
for vcf_line, locus_and_info in zip(vcf_file.readlines(), loci_and_info):