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.
GVCF of amplicon sequencing
I'm trying to generate a GVCF with HaplotypeCaller based on amplicon (PCR) sequencing, and bases towards the end of the reads (~10 bases last bases) consistently get genotype quality of 0, even when the base quality is high. I tried simulating reads, and even if the position is covered by reads from both strands, with a large number of reads, and high base quality the genotype quality of the reference is 0. If there is a SNP in that position, it does get called with reasonable genotype quality, only the reference bases get quality 0. I tried changing various parameters but nothing seems to make a difference? Is there a parameter I'm missing? should I submit a detailed bug report?