Errors loading particular vcf files into IGV but not others

[NBlackburn]

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

[TiborNagy]

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

[NBlackburn]

Nice thinking TiborNagy, but they're all VCF versions 4.1.