Is there a BCFTools command to remove VCF rows missing the GT tag?
Hi everyone,
I have a vcf file that is produced following conversion from a set of .idat files. I find that the GT tag is not properly assigned to each position (potentially reflecting changes in the beadpool manifest file). Since I can't easily fix the error in the .idat to .vcf conversion I want to know if there is a bcftools command to remove rows missing the GT tag altogether.
I can use include/exclude to remove positions where GT=./. but I can't figure out how to remove rows where GT doesn't exist at all.
1 answer
awk -F '\t' '$0 ~ /^#/ || $9=="GT"' in.vcf
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updated
by
GenoMax
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written
by
Pierre Lindenbaum
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written
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Pierre Lindenbaum
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