Re: [Samtools-help] Straight-forward way for strand swapping?

[Christian C. <C....@du...>]

Hi Alec,

Thanks for the response. I was hoping it already existed before diving
into the code.

Will look at this next year.
Regards,

Chris



On 20/12/2013 13:59, "Alec Wysoker" <al...@br...> wrote:

>Hi Chris,
>
>
>No such program exists in Picard, but there it would not be hard for
>someone to write a program using the Picard API.  There are methods for
>reading and writing BAMs, for reverse-complementing sequence, reversing
>qualities, and reversing Cigar also shouldn't
> be hard.  Note that you would also need to fix the reverse-strand and
>mate-reverse-strand flags.  I think that the MPOS field would not need to
>be changed.
>
>
>-Alec
>
>
>
>
>
>On Fri, Dec 20, 2013 at 5:06 AM, Christian Cole
><C....@du...> wrote:
>
>Hi all,
>
>I have some BAM files which, although correctly aligned, have the reads
>assigned to the opposite strand (long story). Is there a tool or function
>in samtools/Picard that simply swaps strands info (incl. rev. complement
>of seq) whilst retaining all the other info?
>
>Many thanks,
>
>Chris
>
>--
>Dr Chris Cole
>Senior Research Associate (Bioinformatics)
>College of Life Sciences
>University of Dundee
>Dow Street
>Dundee
>DD1 5EH
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>
>e-mail: c....@du...
>Tel: +44 (0)1382 388 721 <tel:%2B44%20%280%291382%20388%20721>
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>http://www.researchgate.net/profile/Christian_Cole/
>
>
>
>
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