GATK4 no longer includes CombineVariants

genome / analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

MIT License

102 stars 57 forks source link

Open jasonwalker80 opened 3 years ago

jasonwalker80 commented 3 years ago

A few options (feel free to add more):

Continue to use GATK 3.6 CombineVariants in Somatic/Multi-Caller SNV workflows
Use GATK4 MergeVCFs (or similar) and drop the set annotation from any filters or downstream tools/code
Write a new merge tool, perhaps vatools?, that includes some of the original caller info. See #785

xiucz commented 3 years ago

The set annotation is really helpful to see variants combined by different callers. We can just port it without code changed.

xiucz commented 3 years ago

I have been waiting for this tool to be ported since GATK4 was born. ^_^ .