Hello, I have a BAM file and I want to create another BAM file by filtering only reads that are 100% identical mapped. For example if my read length is 100 , I want to select CIGAR 100M and make a bam file. Could you please suggest how this can be done. Thanks Adrian
Depending on your aligner, NM may or may not include clipped bases so you'll probably want to check the CIGAR as well.