Monday, July 4, 2011

Mendelian Disorder: Accurate genome-wide read depth calculation (how-to using BedTools genomeCoverageBed)

MONDAY, JULY 4, 2011

Accurate genome-wide read depth calculation (how-to)
I'm currently working ferociously on revisions to a paper and need to calculate mean genome-wide read depth as a fine point in the paper. My first inclination was genomeCoverageBed from BEDtools. Trying it out on chromosome 22 first, I noted a huge number (>30%) of the bases had 0 coverage. Of course, this must be because genomeCoverageBed is including the massive centromere (chr22 is acrocentric--the entire p-arm is unmappable heterochromatin). I kind of already knew genomeCoverageBed wasn't meant for this purpose anyway, but I was hoping to stumble upon something.


(Via read more on the original page .)