Attention: Want an end-to-end pipelining solution for GATK Best Practices?
what interval files do you guys use for human exome variant calling?
I downloaded my intervals files from UCSC human exome captured file (hg19_exome_sorted.bed), but I keep getting lots of "./." in the final VCF files. I asked before in this forum, and I remember Geraldine said this may be because of sub-optimal interval files. This made me wonder what you guys use for human exome variant calling?