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.
haplotypecalling of side-by-side variants homo/hetero
we currently observed several cases were we find hetero/homo variants in to continous positions. Looking on the BAM file verifies that the variants are on the same allele/reads.
The GATK HaplotypeCaller will always call these variants as two single variants whereas for example freebayes will call it as a single variant.
e.g. in VCF file format:
10 123123123 G A ...
10 123123124 C A ...
10 123123123 GC AA ...
Why is GATK Haplotypecaller not combining these two variants, since we are interested in the haplotype? Did I miss a flag for the command line etc. ?