What does samtools mean by 'orientation' when marking duplicates?
Entering edit mode
19 months ago
Thomas ▴ 160

Hello Biostars,

It is my understanding that samtools marks duplicates on the basis of the 5' position of reads and also the orientation of reads. This is based on my reading of the following:


However, I am not sure what exactly is meant by 'orientation' in this context.

In my mind, this can be interpreted in two ways:

1) Whether paired end reads are facing inwards, outwards or in the same direction

2) Everything stated above but also whether the set of first reads from a set of paired end reads map to the same strand or not (i.e. F1R2 and F2R1 nomenclature - cf Orientation of PE reads a review of --fr --ff and --rf meanings)

If anybody has any idea about this, that would be great


read_orientation samtools htslib • 726 views
Entering edit mode
18 months ago
aw7 ▴ 130

I had forgotten about that htslib.org page. It is out of date and I really need to rewrite it some time.

Orientation in this case means that the strand and the direction (as well as the unclipped position) need to match for a read to be marked as a duplicate.

Basically the same as in 2) or Bowtie Paired-end options.


Login before adding your answer.

Traffic: 2152 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6