GenomicsDBImport: Attempting to genotype more than 50 alleles

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Nils Homer

• August 06, 2020 00:13

I'm joint calling ~10K samples, where I expected there to be MANY possible alleles/genotypes.  How do I increase the # of alleles supported by GenomicsDBImport? 

Perhaps this one?

--genomicsdb-segment-size?

Related to: https://gatk.broadinstitute.org/hc/en-us/community/posts/360072096991-GenomicsDBImport-has-too-many-genotypes-in-the-combined-VCF-record

a) GATK version used

The Genome Analysis Toolkit (GATK) v4.1.8.1

HTSJDK Version: 2.23.0

Picard Version: 2.22.8

b) Exact GATK commands used

gatk \

           --java-options "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx16g"  \

           --spark-runner LOCAL \

           GenomicsDBImport \

           -L <redacted> \

           --genomicsdb-workspace-path /path/to/db \

           --arguments_file args.txt;

c) The entire error log if applicable.

 

23:36:01.670 WARN MinimalGenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location <redacted>

 

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  Nils Homer

  • August 06, 2020 17:47

  It looks like HTSJDK has the limit:

  https://github.com/samtools/htsjdk/blob/bfb584ed191efdb7b73329f576c4245fc42caf6d/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java#L58

  Here's the place GATK checks:

  https://github.com/broadinstitute/gatk/blob/ca19a404cd218726ee08159005b1a03fd073d997/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java#L331-L339

  But someone thought it might be a command line argument in the future, but didn't wire it to the above the check above:
  https://github.com/broadinstitute/gatk/blob/bc0994c180312cdca7afbe45b410b2c6fc312043/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBArgumentCollection.java#L18-L22

   

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  Genevieve Brandt (she/her)

  • August 10, 2020 20:13

  Hi Nils Homer, I have looked into both of your requests, and unfortunately right now it is not possible to increase the number of alleles supported in GenomicsDB import. One option you might try is to look into the joint-calling WDL https://github.com/gatk-workflows. Using the gnarly genotyper (not genotype GVCFs), you will be able to run your analysis with more alleles. For your current workflow, there is not a good workaround at this point, since this limit involves more than just GATK. 

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