covmed overestimates coverage? about goleft

[brentp]

yeah, I've noticed this as well. I'll have a look today. Picard and bedtools are doing actual coverage calculations across the whole bam (I'm pretty sure, anyway) while covmed is estimating based on a sample, but it still should be able to have a pretty good estimate.

[brentp]

@hdashnow would you give one of the attached binaries a try (I have to gzip to attach here so you'll have to unzip and chmod +x).
This should give a more accurate estimate, but I'd like to see how it performs for your cases.

You can now do : goleft covmed *.bam
so it's easier to run on a group of bams.
goleft_osx.gz
goleft_linux64.gz

[brentp]

and a caveat is that goleft is likely to be inaccurate for exome or targetted, but I'll improve that a bit more in the future.

[hdashnow]

Good idea adding that filter. It made the estimates slightly smaller. e.g. 33.04 instead of 33.4. Still nowhere near Picard.