PyVCF
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DP should be None if no call is made
I ran into the following problem using the latest pyvcf from pip. I should note that this is for the following haploid record.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
gi|194447306|ref|NC_011083.1| 299078 . T A 178.77 . AC=1;AF=1.0;AN=1;DP=8;FS=0.0;MLEAC=1;MLEAF=1.0;MQ=28.13;QD=28.35;SOR=3.611 GT:AD:DP:GQ:PL:FT 1:0,5:5:99:207,0:G_dp10 .:0,0:.:.:.:.
When no call is made, I expected the DP to be set to None
, so that I could do if call.data.GT: do somthing
. However, this doesn't work, because the call.data.GT gets set to .
instead of None
. Is this the expected behaviour? As you can see from the print output, the other fields that have .
in the vcf file are converted to None
.
# No call made
if call.data.GT == '.':
print(call.data)
CallData(GT=., AD=[0, 0], DP=None, GQ=None, PL=None, FT=None)