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genome / analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.
MIT License
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Add copy number to exome/targeted workflows #296

Closed jasonwalker80 closed 5 years ago

jasonwalker80 commented 6 years ago

As far as germline CNV, we will definitely need something other than Varscan. xhmm is what Ira's group has used. We should look into that and ask around for other recommendations. Haley Abel would be a good person to talk to. There is also the GATK machinery. V4 has copy number (https://software.broadinstitute.org/gatk/documentation/article?id=11682)

jasonwalker80 commented 6 years ago

It sounds like the xhmm approach would be a separate joint-calling workflow.

Direct from the docs: XHMM was explicitly designed to be used with targeted exome sequencing at high coverage (at least 60x - 100x) using Illumina HiSeq (or similar) sequencing of at least ~50 samples.

jasonwalker80 commented 5 years ago

For now, this means CNVkit. We can address alternative callers as a separate issue.