search

wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
297 stars 30 forks source link

Extracting bam files #166

Closed ntromas closed 1 year ago

ntromas commented 1 year ago

Hi!

I wonder if the extracted bam files with the following parameter: --bam-file-cache-directory & --discard-unmapped includes the mapped reads from both R1 and R2 (I guess yes but the filename is only using R1 filename) and if the bam file is sorted (to extract mapped reads later for example).

Cheers!

Nico

wwood commented 1 year ago

Hi,

Sorry for the late response here.

Yes is the answer.

HTH, ben