Hi Everyone, I am trying to extract the sequences for my contig from the bam file. Looking at the CIGAR string there can be different cases few of them being:
10S20M 20M10S 10S20M2S 20M1D10M 6M1D15M2D20M
and many more where we have insertions and deletions and of course N(for introns). I made my own custom genome and mapped reads to it. In the bam file, I will have the full read sequence with Soft clipping bases present. But looking them at IGV, I only see the matched part of the CIGAR string. Is there a tool which gives me only the matched part(M) of the CIGAR string and nor Soft clip sequences.