samtools flagstat result is different from samtools view result
1
0
Entering edit mode
7.9 years ago
Louis Kok ▴ 30

Hi All. I wonder if anyone of you have inconsistent mapping result generated by samtools flagstat and samtools view command?

My samtools flagstat output is as below:

3217 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
2788 + 0 mapped (86.66%:nan%)
393 + 0 read1
393 + 0 read2
480 + 0 properly paired (61.07%:nan%)
480 + 0 with itself and mate mapped
148 + 0 singletons (18.83%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

The total mapped reads number is 2788. However, when I did samtools view and do a read count on those mapped to reference, the number was 2936. I wonder why the number is different in this case.

SAMtools • 3.7k views
ADD COMMENT
0
Entering edit mode
> 3217 + 0 in total (QC-passed reads + QC-failed reads)

What represents the number 3217? The total number of reads analized?

ADD REPLY
0
Entering edit mode

What you mean by analyzed? It means in this file there are 3217 reads.

ADD REPLY
0
Entering edit mode

Sorry for the mistake and thank you for the answer. I was a little confused with my own results of flagstat:

6060680 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
6051340 + 0 mapped (99.85%:-nan%)
6060680 + 0 paired in sequencing
3032920 + 0 read1
3027760 + 0 read2
5669320 + 0 properly paired (93.54%:-nan%)
6042000 + 0 with itself and mate mapped
9340 + 0 singletons (0.15%:-nan%)
257886 + 0 with mate mapped to a different chr
28511 + 0 with mate mapped to a different chr (mapQ>=5)
ADD REPLY
5
Entering edit mode
7.9 years ago
Dan D 7.4k

samtools flagstat splits out the reads which mapped as a pair (2,788) vs those which mapped only as singletons (148).

2,788 + 148 = 2,936.

ADD COMMENT
0
Entering edit mode

Thanks Dan for the explanation. For the number of reads mapped, would you take in consideration of singletons as well?

ADD REPLY

Login before adding your answer.

Traffic: 2278 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6