Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
sam to bam conversion error, no @SQ lines in the header, missing header? efoss Bioinformatics 17 12-03-2015 05:28 AM
Find unmapped read from sam/bam file genelab Bioinformatics 9 03-18-2014 02:35 PM
the header of SAM and BAM missing dongshenglulv Bioinformatics 5 10-24-2011 12:44 AM
.SAM to .BAM with SAM file header @PG emilyjia2000 Bioinformatics 13 06-14-2011 01:21 PM
Important fields of SAM file to be considered while compression nadir Bioinformatics 0 03-29-2011 10:58 PM

Thread Tools
Old 05-11-2010, 07:59 AM   #1
Location: Germany

Join Date: Dec 2009
Posts: 11
Default BWA: specifying SAM/BAM file header fields before read alignment?

Dear all,

I have found the modification of SAM/BAM file headers quite cumbersome and time-consuming, so I wonder if it is planned to include an option into BWA to specify header fields before starting the alignment, or if there is a supereasy, superfast way of adding header lines to a SAM or BAM file without overwriting the beginning of the alignment?

Currently I am splitting the output SAM file into header and alignment, modifying the header, and concatenating them back together. This needs about 15 minutes for a 40 million reads SAM-file, which seems a bit much knowing that I only want to add a couple of alignment info lines.

Many thanks!
nora is offline   Reply With Quote
Old 05-11-2010, 11:11 AM   #2
Senior Member
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323

I don't think there are plans to incorporate that feature anytime soon. Feel free to email the mailing list.

Dump your alignments in BAM format and process the header with picard. You should reduce the processing time.
drio is offline   Reply With Quote
Old 05-12-2010, 10:33 AM   #3
Location: Germany

Join Date: Dec 2009
Posts: 11

Thanks for your advice!
nora is offline   Reply With Quote
Old 12-04-2010, 10:11 PM   #4
Location: Toulouse

Join Date: Nov 2008
Posts: 21

did you try "samtools reheader"?
Never used, but seems to do what you want

gerald2545 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:41 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO