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Question for people working with SAM files in genome alignments

by Anonymous Monk
on Dec 21, 2017 at 12:17 UTC ( [id://1205975]=perlquestion: print w/replies, xml ) Need Help??

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Dear friends,
I have started a project in Genomics, which involves using the SAM alignment files. My question is, if any of you has previously succeeded in combining the CIGAR and MD strings from the SAM file in order to reconstruct the alignment. I cannot find some code and I assume this has been done in the past. Any help would be greatly appreciated!
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Re: Question for people working with SAM files in genome alignments
by marto (Cardinal) on Dec 21, 2017 at 16:02 UTC
Re: Question for people working with SAM files in genome alignments
by Laurent_R (Canon) on Dec 21, 2017 at 15:39 UTC
    Hi,

    I am not a geneticist and I don't understand your question.

    As I suppose that many monks here are in a similar situation, it might be worth for you to try to explain what you're trying to do in words that will be understood by people having a limited or no biological background.

      This may be the rare exception to our rules for posting an effective question. The OP appears not to be seeking help with perl progamming, but rather, seeking a tool (possibly written in perl) to solve his genetics problem. I hope that someone will be able to help him.
      Bill
Re: Question for people working with SAM files in genome alignments
by karlgoethebier (Abbot) on Dec 22, 2017 at 20:51 UTC

    I have no clue. But you might take a look at htslib.org and SAMTools. Don't know if this helps. Regards, Karl

    PS.: For the other uninitiated: SAM

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Re: Question for people working with SAM files in genome alignments
by ablanke (Monsignor) on Dec 23, 2017 at 11:37 UTC

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