In the bam_pileup1_t
struct there are two fields, is_del
and indel
. I think I understand is_del
, it means that the read has a deletion at that point in the reference (corresponds to *
in the mpileup output). But what does indel mean?
In the bam_pileup1_t
struct there are two fields, is_del
and indel
. I think I understand is_del
, it means that the read has a deletion at that point in the reference (corresponds to *
in the mpileup output). But what does indel mean?
OK, I now understand. It's funny when you finally ask the question the answer can suddenly become clear. is_del = 1
means that at this position right here the current padded read is a deletion. indel = -k
where k > 0
means that the current read is a deletion at the next k reference positions. indel = k
where k > 0
makes more sense, it means there is an insertion in the current read between this position and the next position.
From the source code:
@field indel indel length; 0 for no indel, positive for ins and negative for del @field is_del 1 iff the base on the padded read is a deletion
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Exactly.