Question

Methods for Doing Consensus Variant Calling between multiple callers

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4.7 years ago

djevanclark ▴ 40

We are currently retooling a pipeline to do consensus calling between 3 variant callers, Mutect2, strelka, and lancets. We would like some thoughts on the best way to do consensus calling on the VCF outputs. We have some older custom scripts that are very convoluted, and have also looked at selectvariants from GATK. Any input is appreciated.

WES DNA Consensus Variant Calling • 1.8k views

ADD COMMENT • link 4.6 years ago by djevanclark ▴ 40

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This work might give some insipration: https://www.ncbi.nlm.nih.gov/pubmed/29945233

ADD REPLY • link 4.7 years ago by ATpoint 82k

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That is what we ended up going with. We are just looking to modify it now to support 3 other variant callers.

ADD REPLY • link 4.7 years ago by djevanclark ▴ 40

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Hi! Have you used ATpoint's solution?

ADD REPLY • link 4.7 years ago by Denis ▴ 310

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We are still trying to get it working, right now we are working to rewrite it into our CWL ecosystem.

ADD REPLY • link 4.7 years ago by djevanclark ▴ 40

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As a side note to this, anyone interested in contributing to this project? i.e. wrapping in CWL. We are a group from Mount Sinai Icahn Medical school and are building a solid repo of CWL wrapped tools with some consistent standards. https://gitlab.com/iidsgt/biowdl

ADD REPLY • link 4.7 years ago by djevanclark ▴ 40

score 2 · Answer 1 · 2019-09-26

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4.6 years ago

djevanclark ▴ 40

We ended up writing our own solution which can be pulled from here. https://hub.docker.com/r/sinaiiidgst/consensus_caller

It's simply invoked by running consensus_caller from bash.

ADD COMMENT • link 4.6 years ago by djevanclark ▴ 40