How to convert heterozygous variants to ./. in a VCF file?
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bcftools +setGT in.vcf -- -t q -i 'GT="het"' -n '.'
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Pierre Lindenbaum
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Hi! What are you trying to achieve? What do you mean by "converting heterozygous alleles to NA"? Could you simply discard them from your VCF? Could you describe your desired output?
I want to mask heterozygous sites and work only with the homozygotes. Thank you for the comment :)
I think if you just need to work with homozygous variant calls, you could simply generate a new VCF with the homozygous calls:
N.B: These commands only work for a single alternative allele at the variant position.
thats very handy, thank you so so much, but I really want to convert heterozygotes to
./.and keep them in the file. Maybe I could try a grep command? Also thank you so much for your time, means a lot learning from othersSure, no worries, happy to help. So, an easy way could be with
sed:NA ? that doesnt fit in the VCF specification. Could be
./.but not NA.Yes you are right to
./.I wanted to write. I am changing the question asap