Recommendations for input vcf

[mrvollger]

Hi @holtjma,

Would you be able to share the DeepVariant parameters and filtering steps you use at PacBio before applying hiphase? I'd like to be as consistent as I can with your process! Sorry if this is documented and I missed it.

Cheers, Mitchell

[holtjma]

Hey Mitchell,

For testing, we've basically been using the pb-human-wgs-workflow-snakemake. The specific DeepVariant part can be found here: https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake/blob/main/rules/sample_deepvariant.smk

Other components, like parameters for pbmm2, can also be found in that repo.

Matt

[holtjma]

I should mention that if you want a simple one-liner based on Docker, then you can use the built-in wrapper command like here:

https://github.com/google/deepvariant/blob/r1.5/docs/deepvariant-pacbio-model-case-study.md

My understanding is that these are equivalent.

[mrvollger]

Awesome! looks like very minimal filtering :)!

Thanks for the quick response.