GenomicsDBImport: has too many genotypes in the combined VCF record

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Nils Homer

• August 06, 2020 00:12
• Edited

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?

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.

Sample/Callset <redacted>( TileDB row idx 6055) at Chromosome chr1 position <redacted> (TileDB column 26661119) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added  for this sample for this location.

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  Nils Homer

  • August 06, 2020 17:54

  Any way to override this in the config?
  https://github.com/GenomicsDB/GenomicsDB/blob/2225b6e19d18cbcf98be52fac4529d9156ba7948/src/main/cpp/src/config/genomicsdb_config_base.cc#L59

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  Genevieve Brandt (she/her)

  • August 10, 2020 20:16

  Hi Nils Homer, I have written a response on your other post that pertains here as well: https://gatk.broadinstitute.org/hc/en-us/community/posts/360072168712-GenomicsDBImport-Attempting-to-genotype-more-than-50-alleles?page=1#community_comment_360012343671

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