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) v18.104.22.168
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.
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