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Methods for Doing Consensus Variant Calling between multiple callers

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
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written by djevanclark • djevanclark

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

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written by djevanclark • djevanclark

Hi! Have you used ATpoint's solution?

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written by Denis Denis

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

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written by djevanclark • djevanclark

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

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written by djevanclark • djevanclark

1 answer

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.

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written by djevanclark • djevanclark

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