Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GnarlyGenotyper (BETA) Follow

1 comment

  • Avatar

    I decided to use GnarlyGenotyper instead of GenomicsDBImport, as the number of genotypes for this last one is limited to 50. A GATK team member as advised to use GnarlyGenotyper in the link below.

    I have been running GnarlyGenotyper with the following flag to allow more alleles.

    --max-alternate-alleles 100

    Unfortunately, I still get this kind of error:

    Chromosome Chr1 position 1158382 (TileDB column 247751759) has too many alleles in the combined VCF record : 9 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

    Is it due to the software, or did I use the wrong flag?


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk