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
(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
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