Jon Puritz

> ### suggestion > apply a minimum coverage filter to the `cov.stats` prior to making the `mapped.*.bed` files, which will ultimately reduce the number of contigs genotyped > > ###...

I'm not sure about shuffling the cov.stats file. Yes, this would distribute the load more evenly, but it achieves this by splitting up high coverage contigs and by breaking up...

It seems odd that you coverage is so low.

Perhaps, we can put in something logical like > 1, but yes anything more should be optional. Jon Puritz, PhD Assistant Professor Department of Biological Sciences University of Rhode Island...

I'd be ok with adding the primary alignments filter to the `cat-RRG.bam` file (I don't think freebayes uses them anyway), but I don't think reads should be filtered on "properly...

73a01502425cfdc812299d98ffcc5f01dd78f468 Should fix this. Please test and let me know.