Best way to combine multiple results from dna-seq-gatk-variant-calling

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Philipp Schneider

• September 06, 2022 07:22

Hey everyone,

I am performing variant call with this GATK pipeline: https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling.

What would be the best way to combine the results of different studies? So let's say this pipeline finished for WES data from one study and from a second one and now I want to combine these (whole exome in both files; different samples). Would `bcftools merge` or `combinegvcfs` work with the final annotated VCFs or should I use VCFs from an earlier step of the pipeline. Or are there better tools to do this with annotated VCFs?

Best and Thanks,

Philipp

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  Genevieve Brandt (she/her)

  • September 06, 2022 21:09

  Thank you for your post, Philipp Schneider! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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