Hi,

I have been running cn.mops successfully and im in the need now to run it again using bam files retrieved from NCBI which are realigned BAM files after the recalibration step (BQSR) recommended from the best practices.

I get an error pointing to the bam file, however the bam file is fine and opens without issues....it seems that cn.mops doesnt run with bam file coming from BQSR step but just raw bam file (before the BQSR step).

Do you have experienced this issue? 

Any suggestion will be highly appreciated,

thanks a lot for your time,

Laura