SEQanswers (
-   Bioinformatics (
-   -   How can I parse these reads (

yksikaksi 04-24-2012 11:21 PM

How can I parse these reads

49080460 + 0 in total
0 + 0 duplicates
6444347 + 0 mapped (13.13%:nan%)
49080460 + 0 paired in sequencing
45547041 + 0 read1 
3533419 + 0 read2 
5822436 + 0 properly paired (11.86%:nan%)  ***
5822436 + 0 with itself and mate mapped
621911 + 0 singletons (1.27%:nan%)

Good day.

I would like to parse the paired reads (***) from PCR duplicates removed sorted BAM files. I knew SAMtools or Picard tools can do that, however, I'm not sure what function or what option I should use.

Could anyone kindly please contribute the idea(s) or command line(s) or advice?

Thank you very much.

maubp 04-25-2012 05:36 AM

PCR duplicates are marked in SAM/BAM as part of the read's FLAG entry (one of the bits).

You can use 'samtools view' with the -f and/or -F switches to filter reads based on their FLAG values.

By default 'samtools view' does BAM to SAM, but it can do SAM to SAM or BAM to BAM as well which is more sensible for filtering.

swbarnes2 04-25-2012 09:44 AM

What exactly are you trying to parse?

You can use samtools view and filter by flags (-f or -F) to break out particular kinds of reads based ontheri flags. You can use samtools view to make a .sam, and pipe that straight into a program like awk or grep.


samtools view file.bam | grep whatever - > grepped.sam

yksikaksi 04-25-2012 11:02 PM

I want to exclude unmapped reads from the PCR duplicates removed BAM file (done by Picard MarkDuplicates tools) before carry on to downstream analysis. Thanks for the replied and suggestions. Appreciate that!

swbarnes2 04-26-2012 09:16 AM


samtools view -bF 4 file.bam > mapped.bam
will make a new .bam that has only mapped reads.

the -F 4 means that it will exclude entries in your .bam that have the 4 flagged in the binary flag; 4 is the code for unmapped read. The -b means that it will output a .bam, instead of a .sam, which is the default behavior for samtools view.

yksikaksi 04-26-2012 11:24 AM

Thanks for the code and the explanation. Thanks a lot.

All times are GMT -8. The time now is 07:54 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.