|
|
|
|
|||||||
Similar Threads
|
||||
| Thread | Thread Starter | Forum | Replies | Last Post |
| How to extract mapped and unmapped raw reads from bwa's sam file ? | vaibhavvsk | Bioinformatics | 11 | 02-07-2013 10:01 AM |
| Extract perfectly mapped reads from SAM/BAM file | Graham Etherington | Bioinformatics | 2 | 07-21-2011 08:27 AM |
| SAM/BAM how to retrieve all mapped reads ? | Sylphide | Bioinformatics | 2 | 05-31-2011 07:57 AM |
| Filter paired end BAM file based on iSize | Leif Bergsagel | Bioinformatics | 2 | 12-16-2010 12:50 PM |
| How to filter rRNA reads in SAM file. | townway | Bioinformatics | 3 | 07-15-2010 08:54 AM |
 |
|
|
Thread Tools |
06-18-2012, 01:36 AM
|
#1 |
|
Member
Location: Earth Join Date: Mar 2012
Posts: 11
|
Filter paired & mapped reads from SAM/BAM file
Hi,
I have SAM/BAM files of paired end Illumina sequencing obtained by BWA. I want to filter out all reads having "proper pair" and both the reads of pair aligned to references. How can I filter them?  Thanks in advance... |
|
|
|
06-18-2012, 07:13 AM
|
#2 |
|
Senior Member
Location: Cambridge, UK Join Date: May 2010
Posts: 311
|
Hi- This should filter out all the reads where both mates are mapped and the mates face each other (---> <---). (Make sure it does what you want!).
Code:
samtools view -F 2 input.bam > output.sam Dario |
|
|
|
|
06-19-2012, 02:21 AM
|
#3 |
|
Member
Location: Earth Join Date: Mar 2012
Posts: 11
|
Thats what I was looking for!
Thank you Dario for the reply. I was looking for the same.
|
|
|
|
|
| Thread Tools | |
|
|
