Hi, I am trying to filtering a vcf file by --minDP however the log file indicates that it is not filtering out any SNP, any clue about this problem? I tried different values for DP but is not working any of them (I do have DP information in my vcf file)
I have a script that can do what you need.
vcf_reader = vcf.Reader(open("file.vcf", 'r'))
vcf_writer = vcf.Writer(open('out.vcf', 'w'), vcf_reader)
for record in vcf_reader:
Hope it helps,