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  • Errors loading particular vcf files into IGV but not others

    Hi,

    (would've posted this in the google group but it's not letting me for some reason, so I thought I'd try SEQanswers instead)

    IGV version: 2.2

    What I did:
    - File -> Load from file -> indels.vcf

    What I expected to happen:
    Loading of indel variations into track of IGV browser

    What actually happened:
    Error loading /filepath/Indels.vcf: Line: chr1 821351 . TGCTGTGGTT----- TAGGGCTGATATGGA 357 PASS DP=55 GT:GQ 0/1:357

    Thought it might be a problem with the index for this vcf file, so reindexed it with igvtools and the following error came up whilst running igvtools:
    Error: Line: chr1 821351 . TGCTGTGGTT----- TAGGGCTGATATGGA 357 PASS DP=55 GT:GQ 0/1:357

    This is an Illumina generated file, I have other vcf files from other individual vcf files from the same batch that load into IGV fine (and some that have similar errors including: Error: The provided VCF file is malformed at approximately line number 110: Unparsable vcf record with allele TGCTGTGGTT----- when using igvtools to index).

    This file and others have loaded fine into previous versions of IGV. I just haven't accessed it for a while.

    Any thoughts on what's going wrong?

    Cheers,

    Nick
    Nicholas Blackburn | PhD Candidate
    Tasmanian Inherited Cancer Centre
    Menzies Research Institute Tasmania
    Hobart TAS 7000 | www.menzies.utas.edu.au

  • #2
    Maybe it is an old VCF format? IGV 2.2 read VCF version 4.0.

    Comment


    • #3
      Nice thinking TiborNagy, but they're all VCF versions 4.1.
      Nicholas Blackburn | PhD Candidate
      Tasmanian Inherited Cancer Centre
      Menzies Research Institute Tasmania
      Hobart TAS 7000 | www.menzies.utas.edu.au

      Comment

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