Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

      Latest Articles

      Collapse

      • seqadmin
        New Genomics Tools and Methods Shared at AGBT 2025
        by seqadmin


        This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

        The Headliner
        The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
        03-03-2025, 01:39 PM
      • seqadmin
        Investigating the Gut Microbiome Through Diet and Spatial Biology
        by seqadmin




        The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
        02-24-2025, 06:31 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 12:50 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-03-2025, 01:15 PM
      0 responses
      181 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-28-2025, 12:58 PM
      0 responses
      275 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-24-2025, 02:48 PM
      0 responses
      663 views
      0 likes
      Last Post seqadmin  
      Working...
      X