Looking for a function like GenotypeGVCFs in Hail

Hail Query & hailctl
1

Hello,

I am trying to do joint-calling for 10k gvcfs (maybe more). First, I am combining a bunch of gvcfs to one MT using the ‘vcf_combiner’ function in Hail. After gvcf-combining, I am wondering if I can run a process like GenotypeGVCFs in GATK inside Hail.

Thanks,

Jina

2

Thank you for your question and it’s exciting to know that we have another vcf_combiner user.

Just out of curiosity so that we can help you better, what will you want to use GenotypeGVCF for in your analytical pipeline? To subset for VCFs or specific IDs?

3

Hello Kumar,

Thank you for your reply. I am expecting the joint-VCF in which the values of unreliable calls are filtered or adjusted. Actually, I just started to apply joint-genotyping in our WGS pipeline recently and am still studying about joint-genotyping. So this answer maybe not practical, but conceptual. I am looking forward to your advice. Thank you.

Best,
Jina

4

For this, I think our team expert on this may be of help. @chrisvittal?

5

Thanks, @kumarveerapen and @chrisvittal. I hope I can get some advice to build a joint-genotyping process.

6

We do not currently have a joint genotyping solution.

We make the assumption that the individual variant calls present in the GVCFs are good.

7

Hi @chrisvitta, Thank you for your reply.