extracting matched part(M) only for the sequence from the CIGAR string

Question

[Varun Gupta]

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.

Thanks

[Devon Ryan]

Have you tried coding something in python with pysam? That'd allow doing this and outputting in whatever sort of format you need.

[Varun Gupta]

Hi Devon, I looked at pysam, but did not find a tool already. May be I will have to look at the syntax and try coding in python. But I thought this was easily available

[Pierre Lindenbaum]

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.

I don't understand what you really need here: why discarding sequences that you don't already see in IGV ?