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?
My setup: ~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?