INNER CODE UNIT · Python
PrintVCFHeader
aquaskyline/Clairvoyante · clairvoyante/callVar.py:156
def PrintVCFHeader(args, call_fh):
print >> call_fh, '##fileformat=VCFv4.1'
print >> call_fh, '##FILTER=<ID=PASS,Description="All filters passed">'
print >> call_fh, '##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold.">'
print >> call_fh, '##ALT=<ID=DEL,Description="Deletion">'
print >> call_fh, '##ALT=<ID=INS,Description="Insertion of novel sequence">'
print >> call_fh, '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">'
print >> call_fh, '##INFO=<ID=LENGUESS,Number=.,Type=Integer,Description="Best guess of the indel length">'
print >> call_fh, '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">'
print >> call_fh, '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">'
print >> call_fh, '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">'
print >> call_fh, '##FORMAT=<ID=AF,Number=1,Type=Float,Description="Estimated allele frequency in the range (0,1)">'
if args.ref_fn != None:
fai_fn = args.ref_fn + ".fai"
fai_fp = open(fai_fn)
for line in fai_fp:
fields = line.strip().split("\t")