Generation of allsites vcf from joint-genotyped samples

[echille]

Hello!

I am trying to run a tool, pixy that requires the use of an AllSites VCF (a VCF that contains all invariant sites in addition to variant sites). I've tried following the Best practices for multi-sample variant calling with DeepVariant workflow, but it seems that it does not support this functionality. Do you have any suggestions on how to generate the AllSites VCF using the DeepVariant workflow? Or could this potentially be added as a future feature?

Thanks!
Erin

[kishwarshafin]

@echille ,

I believe you need VCF and GVCF to follow the steps there.

Please see here and use this following parameter to generate a GVCF:

  --output_gvcf=/output/YOUR_OUTPUT_GVCF \

Then you can use the steps in here https://pixy.readthedocs.io/en/latest/generating_invar/generating_invar.html#generating-allsites-vcfs-using-gatk with the same GVCF produced with DeepVariant. We don't have any specific tool to generate all site vcfs for this, you can produce the VCF and GVCF and proceed accordingly.