I have 5 samples that were sequenced with SeqCap EZ Human Exome Library v2.0 kit from Roche/NimbleGen. I ran it with BWA for alignment and converted to BAM files. Using "samtools depth" I extracted the coverage/depth of all on-target bases, and used it to count how many bases we have on-target.
Interestingly enough, the website of Roche said the kit covers regions of total length of 44.1 million bases, while my samples have between 46 and 47 million on-target bases.
Does anyone know how this is possible?
Interestingly enough, the website of Roche said the kit covers regions of total length of 44.1 million bases, while my samples have between 46 and 47 million on-target bases.
Does anyone know how this is possible?