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Old 05-11-2010, 06:59 AM   #1
nora
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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!
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