Filter vcf file by position AND alternative allele
I am filtering a vcf file this way:
bcftools view -R file.pLoF.tsv -Oz -o filtered.pLoF.vcf.gz c12.vcf.gz
However this filters by position, regardless of which ALT allele. How can I enforce this to keep this:
chr12:20875274:G:GT
and leave out this:
chr12:20875274:G:C
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_quantum_girl_ •
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use bcftools isec
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Pierre Lindenbaum
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