How is vcf-merge handling different INFO for a single variant?

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4.5 years ago

Cindy ▴ 40

I imputed several different datasets with the Michigan imputation server and downloaded the output dose.vcf.gz files. I then merged them together by chromosome. I have used both vcf-merge and bcftools merge. My question is, for the same variant, r-square imputation quality can be different between datasets; how is these merging commands dealing with that? I think this is important for downstream analysis. Thanks in advance!

RNA-Seq vcfools bcftools imputation • 1.5k views

ADD COMMENT • link 4.5 years ago by Cindy ▴ 40

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Please read the bcftools manual:

-i, --info-rules -|TAG:METHOD[,…] Rules for merging INFO fields (scalars or vectors) or - to disable the default rules. METHOD is one of sum, avg, min, max, join. Default is DP:sum,DP4:sum if these fields exist in the input files. Fields with no specified rule will take the value from the first input file. The merged QUAL value is currently set to the maximum. This behaviour is not user controllable at the moment.

ADD REPLY • link 4.5 years ago by Ram 44k

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Thank you! Exactly what I was looking for. I just want to confirm vcf-merge is following the same default, getting INFO from the first input file. I couldn't find it in the vcftools documentation.

ADD REPLY • link 4.5 years ago by Cindy ▴ 40

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AFAIK vcftools is obsolete, there's no feature that bcftools or other tools such as vt/GATK SelectVariants don't cover.

ADD REPLY • link 4.5 years ago by Ram 44k

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