I used the expanded exome kit (nextera) for my samples. Now I want to use picard/HsMetrics, which asks for a baits and targets files.
On the Illumina website, I can find the targets bed file for the kit. I also find the targeted_regions file.
Are these the correct files for picard HsMetrics? When I use them, I get strange values for efficiency (like >2).
Maybe the targets file is some sort of "expanded exome definition"? if so, how do i find this definition for "expanded exome / illumina"? if the targets is this "exome definition", what is the the baits file? (would it be the targets file provided by illumine?)
Sorry for the naive question, thank you