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  • bwa map single and PE reads to ref?

    Hello,

    I want to store detect my variants in a VCF format. For that I need to map my PE reads (100x2) to reference. What I have discovered however is that for a lot of my PE reads, the fragments size is smaller than 200bp, which means some PE reads overlap, increasing the coverage of a region artificially.

    I thought I would merge the PE reads with SeqPrep to place all PE reads that overlap in a merged.fastq file.

    My question is, how do I then map both unmerged PE reads and merged SE reads to the genome with bwa? I only know how to do it if it's only SE or only PE.

    Also, does this approach sound reasonable?

    Adrian

    Biostar: http://www.biostars.org/p/97423/#97430

  • #2
    Map the single-ended reads, then map the paired reads, then merge the two sam files. We do that all the time.

    Comment


    • #3
      Sorry I have never merged 2 sam files together, how would I do that?
      Code:
      cat *.sam > new.sam
      ?

      Thanks for the advice!

      Comment


      • #4
        Try samtools merge.

        Comment


        • #5
          As I mentioned on Biostars, just use a variant caller that isn't confused by paired-end reads. GATK is one such example.

          Comment

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