Extract the mapped portion of the read sequence

Question

[rubic]

Probably an easy one.

I'm interested in extracting from a bam file only the portions (i.e., sequence) of a read that match and mismatch the reference, i.e., excluding the clipped positions.

Any idea?

Answer 1

[ATpoint]

Unsurprisingly Pierre Lindenbaum has a jvarkit extension for just that:

Remove Soft Clipped Bases