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.
Missing data in HaplotypeCaller
I have an issue with HaplotypeCaller and its use to call SNPs in RAD data.
I recently used HaplotypeCaller to call SNPs in 600 samples + 50 subspecies samples. Worked fine.
After adding more data to 1200 samples + 120 subspecies samples, ~100 of these subspecies results in 0 calls and just missing data "./." at these loci. Recall that some of these samples and sites were analyzed and called in the first analysis. Any ideas why?
~1200 Read Reduced bam files
Merged into 1 bam file with proper RG headers.
Should I not have merged? Should I not have Reduced Reads?