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Old 03-04-2010, 01:18 AM   #1
bair
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Location: London

Join Date: Jan 2010
Posts: 65
Default samtools flagstat

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
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Old 03-04-2010, 02:35 PM   #2
drio
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Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

Quote:
Originally Posted by bair View Post
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.
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Old 05-28-2010, 03:07 AM   #3
bair
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Location: London

Join Date: Jan 2010
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Default

Quote:
Originally Posted by drio View Post
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.
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Old 05-28-2010, 06:15 AM   #4
drio
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Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
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Quote:
Originally Posted by bair View Post
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.
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