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Support for gVCF merging and genotyping (e.g. CombineGVCFs and GenotypeGVCFs) #1312

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NeillGibson opened this issue Dec 12, 2016 · 3 comments
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@NeillGibson
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@NeillGibson NeillGibson commented Dec 12, 2016

Hi,

Are you planning to support gVCF merging and genotyping on Spark / Adam?

As far as I know the only way to variant call 100K samples is trough creating gVCF files per sample and subsequent gVCF merging and genotyping.

The most well known / production ready implementation of this is from the Broad in GATK:

CombineGVCFs
https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineGVCFs.php

GenotypeGVCFs
https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php

For variant calling of the the 100K+ samples in Exac/GnomAD the first merge step was replaced with GenomicsDB from intel. As I understand it GenomicsDB efficiently stores per sample gVCF tracks and can then efficiently stream merged VCF into GenotypeGVCFs

Broad/Intel GenomicsDB
https://github.com/Intel-HLS/GenomicsDB
https://vimeo.com/194823486/506da42daf (from minute 19)

Genomics DB is based on Intel TileDB
http://istc-bigdata.org/tiledb/index.html

Something similar to CombineGVCFs/GenotypeGVCFs/GenomicsDB is being developed by DNAnexus that also supports on demand joint genotyping from Freebayes gVCF:

GLnexus
https://github.com/dnanexus-rnd/GLnexus

Are you also planning scalable gVCF storage and on demand gVCF merge and joint genotyping on top of Spark / Adam?

Thank you.

fnothaft added a commit to fnothaft/avocado that referenced this issue Oct 15, 2017
Resolves bigdatagenomics/adam#1312. Enables gVCF style data to be used with the
joint variant caller by extracting the sites where a variant was called as a
genotype in one of the gVCFs. These variant sites are then joined back against
the original genotypes. If the genotyped allele was not present and a reference
model block is present, the allele is extracted out from the reference model.
@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
@ggittu
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@ggittu ggittu commented Oct 3, 2018

@heuermh @fnothaft Is there any document that says how to use CombineGVCFs and GenotypeGVCFs in ADAM (spark way)?

@ggittu
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@ggittu ggittu commented Oct 3, 2018

@heuermh Got it. So i will run something like

avocado-submit jointer -from_gvcf /vcf/*.gvcf /output

Here I think the jointer is for CombineGVCFs , what is the one I can use for GenotypeGVCFs?

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