Re-write strand information in BAM file

droog_22 · 11-04-2011, 08:01 AM

Hello,

I have a quick and simple questions: Is there a ready-to-use tool which allows me to re-write the strand information in a BAM file, such that reads which mapped on the forward strand are stored as mapping to the reverse strand and vice-versa?

I know how to do it with samtools and awk, but I was wondering if there was a faster solution without going through an intermediate SAM file.

Cheers, Daniel

maubp · 11-07-2011, 04:25 AM

I'm not quite sure what you are trying to do (or why), but in principle if you can program in Java you should be able to do this via Picard, or using the samtools C API, perhaps via Python (pysam) or a similar language specific wrapper.

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11-04-2011, 08:01 AM	#1
droog_22 Member Location: Vienna Join Date: Nov 2010 Posts: 10	Re-write strand information in BAM file Hello, I have a quick and simple questions: Is there a ready-to-use tool which allows me to re-write the strand information in a BAM file, such that reads which mapped on the forward strand are stored as mapping to the reverse strand and vice-versa? I know how to do it with samtools and awk, but I was wondering if there was a faster solution without going through an intermediate SAM file. Cheers, Daniel

11-07-2011, 04:25 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	I'm not quite sure what you are trying to do (or why), but in principle if you can program in Java you should be able to do this via Picard, or using the samtools C API, perhaps via Python (pysam) or a similar language specific wrapper.