Outputting both VCF and gVCF

Healthcare & Life Sciences Parabricks
1

Hello! Loving Parabricks so far, incredibly helpful and easy to use.

In germline runs that include DeepVariant, I am looking for a way to output both (1) VCF and (2) gVCF from DeepVariant. I have not figured out a way to do this, and the AI docs helper claims I need to pick one or the other. When running outside of parabricks (using google container), this works without issue, as you may just explicitly set the outputs for each file and get both.

It is pretty helpful to get both, rather than only one without the other. How can I make this happen?

Older, unanswered post here: Output both VCF and gVCF when using deepvariant

2

Have you tried to set just gVCF? I have not verified but Im pretty sure if you set gVCF, it will output VCF next to it

3

It appears you can only choose one or the other, only the google version allows both

4

Hi Peter,

I just quickly tested our Parabricks 4.7 release with running deepvariant like this:

pbrun deepvariant --ref /w/ref.fasta --in-bam /w/input.bam --out-variants out.g.vcf --gvcf

And I got both gvcf (“out.g.vcf“) and vcf (“out.vcf“) file output, sitting next to each other. If you are seeing something different please share your command so we can try to reproduce from our side.

Thanks.

5

Thank you for checking!

It would appear that yes, I get a gvcf and vcf when running deepvariant directly. I seem to have this issue when running deepvariant_germline only. For unrelated reasons I’ve switched to running the germline steps independently anyways, so this is solved for my case!