Best tool to merge .vcf files from different variant callers?

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4.6 years ago

j.lunger18 ▴ 30

I have vcfs from the same samples that have variants called from one of three callers. I want to put these files together so that I can annotate them together. Is there a known best way to do this?

VCF GATK annotation variants SNP • 1.4k views

ADD COMMENT • link updated 4.4 years ago by Biostar 20 • written 4.6 years ago by j.lunger18 ▴ 30

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You're looking for bcftools concat (manual). I don't think combining calls from different callers is recommended though.

ADD REPLY • link 4.4 years ago by Ram 44k

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