Option to produce percent identity summary

[edgraham]

Hello,

I have been using CoverM often for filtering my BAM files based on read percent identity. I am wondering if there is any possibility of adding an option to output a summary indicating the percent identity of every mapped read and the location on the contig/genome that read mapped. I have been developing a manual script to do this in pysam by parsing the CIGAR and MD Tags but considering CoverM already makes some of those calculations for the filtering function it would be great to be able to just output a summary in one step when I filter my BAM files using CoverM.

-Elaina

[jianshu93]

Hello Elaina,

I am also doing similar work for recruitment plot. (reads mapped position, identity et.al. for plotting). Can we work together? Also see our way of calculating trimmed_mean, we call it truncated average depth: https://github.com/jianshu93/Competitive_mapping

thanks,

Jianshu