Question: samtools flagstat result is different from samtools view result
0
gravatar for Louis Kok
3.1 years ago by
Louis Kok10
Singapore
Louis Kok10 wrote:

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 • 1.8k views
ADD COMMENTlink modified 3.1 years ago by Dan D6.7k • written 3.1 years ago by Louis Kok10
4
gravatar for Dan D
3.1 years ago by
Dan D6.7k
Tennessee
Dan D6.7k wrote:

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 COMMENTlink modified 3.1 years ago • written 3.1 years ago by Dan D6.7k

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

ADD REPLYlink written 3.1 years ago by Louis Kok10
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