Question: Methods for Doing Consensus Variant Calling between multiple callers
1
gravatar for djevanclark
11 months ago by
djevanclark40
djevanclark40 wrote:

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.

dna variant calling wes consensus • 515 views
ADD COMMENTlink modified 10 months ago • written 11 months ago by djevanclark40

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

ADD REPLYlink written 11 months ago by ATpoint36k

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

ADD REPLYlink written 11 months ago by djevanclark40
1

Hi! Have you used ATpoint's solution?

ADD REPLYlink written 11 months ago by Denis190
1

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

ADD REPLYlink written 11 months ago by djevanclark40

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 REPLYlink written 11 months ago by djevanclark40
2
gravatar for djevanclark
10 months ago by
djevanclark40
djevanclark40 wrote:

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 COMMENTlink written 10 months ago by djevanclark40
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