I am not sure If am using write terminology or asking my question in a right way. So please do not judge this post early :-). I have a list of Copy Number Variations (CNVs), and I was curious to know if these regions are in the coding part of genomes (exome regions) and if so, how much my exome data are covering those regions.
To answer my question, I used "DepthOfCoverage" from GATK and ran it using hg19 references; so for one of the regions "chr15 20549990 22285350" (which is also a large one!) I got the following error.
##### ERROR MESSAGE: Badly formed genome loc: Contig 16 given as location, but this contig isn't present in the Fasta sequence dictionary
my interpretation for the error is that, this region is not entirely in an exome ... 1) is my interpretation that correct ? 2) is there any other way to answer my initial question ?! (how much my exome data are covering those CNVs?