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  • Help with a probably bad variant call

    Hello all,

    i have a variant from a ION PGM sequencing, called with the ION Torrent variant caller plugin

    CHR POS ID REF ALT

    chr22 44324726 . T TG
    The flow cell evaluator say this is a insertion

    GT:AOP:FAO:FDP:FRO:FSAF:FSAR:FSRF:FSRR:GQ:RO:SAF:SAR:SRF:SRR
    1/1:5:27:27:27:0:16:11:0:0:11:22:0:5:16:6
    You see FSAF = 16, FSAR = 11, FSRF = 0, FSRR = 0, but the observations are

    SAF = 0, SAR=5, SRF=16, SRR=6

    if i look the alignment in IGV i see the following




    i check in dbSNP and in the position 44324727 a well known C/G snp 1KG MAF G=0.284 rs738409

    and the T variant at position 44324730 is also known rs738408



    So in my opinion is more likely a C/G rs738409 SNP, than a novel insertion, and even more it looks like a strand bias because the observed alternate allele as an insertion is only in the reverse strand.



    What's you opinion?
    Last edited by c_ro87; 10-03-2014, 06:51 AM.

  • #2
    cross posted: https://www.biostars.org/p/114559/

    Comment


    • #3
      how i delette this?

      Comment

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