Question: Samtools stats "inward oriented pairs" - what flags does this correspond to?
0
gravatar for roryC
2.1 years ago by
roryC0
University of Edinburgh
roryC0 wrote:

Hi,

I'm trying to understand how Samtools stats designates mapped reads as "inward oriented pairs". I have a mate-pair library contaminated with paired end reads, so I would like to extract the PE reads as an independent file. So far I have the following based on flags and insert sizes:

FLAG 83, Insert is negative

FLAG 163, Insert is positive

FLAG 99, Insert is positive

FLAG 147, Insert is negative

The number of reads I get based on the above is ~5% less than that given in the stats output. Any ideas what else is included, or suggestions for how to do this completely differently?

Cheers!

bam sam samtools sequence alignment • 1.0k views
ADD COMMENTlink modified 20 months ago by vo20 • written 2.1 years ago by roryC0
0
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

Perhaps you have duplicates marked and are literally looking for 83/163/99/147. That'd explain an underestimate.

ADD COMMENTlink written 2.1 years ago by Devon Ryan93k
0
gravatar for vo2
20 months ago by
vo20
UK/Hinxton/Sanger
vo20 wrote:

INWARD = 83, 99, 147, 163 and duplicates (+1024 to any).


OUTWARD = 81, 97, 145, 161 and duplicates (+1024 to any), which are pairs not properly aligned (missing flag 0x2).


OTHER = 65, 113, 129, 177 and duplicates (+1024), which are pairs with both reads in the same direction. You can check what the flags mean here.

ADD COMMENTlink modified 20 months ago • written 20 months ago by vo20
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