Methods for Doing Consensus Variant Calling between multiple callers

Question

[djevanclark]

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.

[ATpoint]

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

[djevanclark]

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

[Denis]

Hi! Have you used ATpoint's solution?

[djevanclark]

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

[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

Answer 1

[djevanclark]

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.