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.
Does HaplotypeCaller detect SNPs which are heterozygous (not matching the refrence allele)?
Dear GATK team,
I have a simple question regarding the HaplotypeCaller/UnifiedGenotype module. There are 3 options for SNPs in the output depended on the reference.
Homozygous for the reference, heterozygous for the reference and alternate nucleotide and homozygous for the alternate nucleotide (0/0, 1/1, 0/1). But what if I would like to have the SNPs which are heterozygous and do not match the reference allel. So e.g. the reference has an A and the mapped reads indicate a G/T. Does one of the module detect that? I have a diploid species and want to get all SNPs. This issue popped up after I had a look on the output of both modules.
Thanks a lot.