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  • a quick question about SV type in pindel?

    just saw several SVs are marked with SVTYPE=RPL - what does RPL stand for?
    couldn't find any clue from pindel website.

    Thank you

  • #2
    I think that's when there are multiple successive bases that are changed, ie, if the reference sequence is:

    AGCGAG,TGAT,GAC

    Then the variant sequence could be

    AGCGAG,CTA,GAC

    At least that's what I remember thinking it was long ago; if that makes no sense then let me know as I could be mistaken for sure.

    Comment


    • #3
      Hi, Thanks a lot for your reply. I ran pindel and was got confused by the first SV output marked with RPL - e.g.

      line306 frameshift substitution KIAA1751:NM_001080484:exon18:c.2194_2215CCAAGCCAGGGTGGGCGGGG, chr1 1887091 1887112 CGCCCGCCCACCCTGGCTTGGC CCCCGCCCACCCTGGCTTGG

      If we align the 2 sequences (ref and alt), apparently it results from a G-deleteion at the 2nd base from the reference sequence. but pindel said it is a RPL

      I ran GATK, which also reported this SV but correctly identified this SV as 'deletion' -
      line253 frameshift deletion KIAA1751:NM_001080484:exon18:c.2214delC.G738fs, chr1 1887092 1887092 G

      I am just not sure if this is because of what I've missed in RPL definition, or because the program was confused by the alignment.

      Comment


      • #4
        Then perhaps I'm a bit confused. The Pindel authors are nice/quick with responses to email inquiries; I'd just email the contact author if I were you.

        Comment


        • #5
          Thank you, Heisman. I just emailed the author, and will update you if there is any response.

          Comment


          • #6
            About svtype in vcf file

            Originally posted by caswater View Post
            just saw several SVs are marked with SVTYPE=RPL - what does RPL stand for?
            couldn't find any clue from pindel website.

            Thank you
            Dear everyone,
            I recently was doing something about genome-wide polymorphism detection, and one of my colleague recommended me to use pindel to get structure variation of re-seq data against reference genome. Here is my question: what does the SVTYPE=RPL in the vcf file stand for?
            Your answer will be useful to me. Thank you!

            Comment

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