Extract the mapped portion of the read sequence

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?

bam rna-seq cigar

• 935 views • link

updated 4.6 years ago by ATpoint

• written 4.6 years ago by rubic

1 answer

Unsurprisingly Pierre Lindenbaum has a jvarkit extension for just that:

Remove Soft Clipped Bases

• 0 views • link

written 4.6 years ago by ATpoint

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