Is it possible to add variant type "VT" to each variant in vcf?

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2.5 years ago

optimistsso4co3 ▴ 130

I tried the following line:

bcftools +fill-tags test.vcf -Ov -o testVT.vcf -- -t VT

But get an error

Error parsing "--tags VT": the tag "VT" is not supported

Is it possible to add variant type annotation to vcf? How to do that? My INFO field contains things like VQSRTrancheSNP99.80to100.00 or VQSRTrancheINDEL99.00to100.00 which indicates the variant type (SNP and INDEL), maybe it's possible to extract it?

Thanks guys.

bcftools • 845 views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 2.5 years ago by optimistsso4co3 ▴ 130

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You should be able to use bcftools query to extract the VQSRTranche... field (along with CHR POS REF and ALT) and then use bcftools annotate to add a modified version of the extracted field as a new annotation.

bcftools might also have an intrinsic SNP/INDEL annotation protocol, plus using REF and ALT lengths might be an option too.

ADD REPLY • link 2.5 years ago by Ram 44k

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