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  • #1

    Roche NimbleGen number of bases

    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?
    "Though it may seem that all's been said and done, originality still lives on" - some unoriginal guy who had nothing better to write as his signature
    Tags: count, nimblegen, roche, target enrichment
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