BWA: specifying SAM/BAM file header fields before read alignment?

nora · 05-11-2010, 07:59 AM

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!

drio · 05-11-2010, 11:11 AM

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.

nora · 05-12-2010, 10:33 AM

Thanks for your advice!

gerald2545 · 12-04-2010, 10:11 PM

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

Gerald

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05-11-2010, 07:59 AM	#1
nora Member Location: Germany Join Date: Dec 2009 Posts: 11	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!

05-11-2010, 11:11 AM	#2
drio Senior Member Location: 41°17'49"N / 2°4'42"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. __________________ -drd

05-12-2010, 10:33 AM	#3
nora Member Location: Germany Join Date: Dec 2009 Posts: 11	Thanks for your advice!

12-04-2010, 10:11 PM	#4
gerald2545 Member Location: Toulouse Join Date: Nov 2008 Posts: 21	Hello did you try "samtools reheader"? Never used, but seems to do what you want Gerald