rmdup: FR orientation, ISIZE

Azazel

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Join Date: Oct 2010

Posts: 52
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rmdup: FR orientation, ISIZE

05-30-2011, 11:07 PM

Regarding rmdup, the manual page (version 0.1.10) for samtools at http://samtools.sourceforge.net/samtools.shtml states that:

In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set.

Assuming that ISIZE is what's called TLEN in SAM Spec v1.4 (the spec and manpage currently linked to from the main samtools web page are apparently inconsistent, took me a while to figure that out).

My questions:

What is "FR orientation"?

The bam-files I work with are bwa output. How can I know if ISIZE is correctly set (or, why should it not be correctly set)?
Tags: rmdup, samtools

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