File: filter-cyvcf2.py

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cyvcf2 0.31.4-1
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import sys
import cyvcf2
n = 0
for v in cyvcf2.VCF(sys.argv[1]):
    if len(v.ALT) > 1: continue
    if v.QUAL < 20: continue
    if v.aaf > 0.05: continue
    n += 1
print(n)