samtools flagstat

[bair]

Hello all,

My merged bam file is about 7.4G,

"samtools flagtstat" shows that:

0 QC failure
0 duplicates
151038423 mapped (95.66%)
157886180 paired in sequencing
78943090 read1
78943090 read2
143478844 properly paired (90.87%)
148750146 with itself and mate mapped
2288277 singletons (1.45%)
3935010 with mate mapped to a different chr
1280027 with mate mapped to a different chr (mapQ>=5)

After run samtools rmdup, I got 7.2G bam file, there are reads removed.

Any explanation for this?

Does "singletons" here mean no paired read in read1 or read2 files?

Thanks

[drio]

Hello all,

My merged bam file is about 7.4G,

"samtools flagtstat" shows that:

0 QC failure
0 duplicates
151038423 mapped (95.66%)
157886180 paired in sequencing
78943090 read1
78943090 read2
143478844 properly paired (90.87%)
148750146 with itself and mate mapped
2288277 singletons (1.45%)
3935010 with mate mapped to a different chr
1280027 with mate mapped to a different chr (mapQ>=5)

After run samtools rmdup, I got 7.2G bam file, there are reads removed.

Any explanation for this?

Does "singletons" here mean no paired read in read1 or read2 files?

Thanks

The author(s) (Heng) specifically recommends moving away from samtools rmdup and use picard.

[bair]

The author(s) (Heng) specifically recommends moving away from samtools rmdup and use picard.

I marked the duplicates by picard, samtools flagstat can detect the number of duplicates, but still cannot find the number of QC failure.

Samtools pileup with -m [1796] is said to have the ability to filter out QC failure and duplicates. How can I know reads with QC failur are removed since flagstat does not find one?

Thanks.

[drio]

I marked the duplicates by picard, samtools flagstat can detect the number of duplicates, but still cannot find the number of QC failure.

Samtools pileup with -m [1796] is said to have the ability to filter out QC failure and duplicates. How can I know reads with QC failur are removed since flagstat does not find one?

Thanks.

Perhaps you don't have QC failure reads? If the flag is steup properly
samtools will filter them out for sure.