Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
I've run the GATK best practices pipeline up through VQSR and have the recalibrated variants in a VCF file. Because I'm analyzing pedigree samples, I'm now attempting to run CalculateGenotypePosteriors. When I do this, I get the following error:
ERROR MESSAGE: Variant does not contain the same number of MLE allele counts as alternate alleles for record at 1:768589
However, when I looked at that variant in the recalibrated VCF file, I see that MLEAC=1, AC=1, and I can confirm that there is only one sample that is heterozygous, so both AC and MLEAC are correct.
Might this be a bug?