GenomicsDBImport: has too many genotypes in the combined VCF record
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?
a) GATK version used
The Genome Analysis Toolkit (GATK) v184.108.40.206
HTSJDK Version: 2.23.0
Picard Version: 2.22.8
b) Exact GATK commands used
--java-options "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx16g" \
--spark-runner LOCAL \
-L <redacted> \
--genomicsdb-workspace-path /path/to/db \
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.
Any way to override this in the config?
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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