whitespace in INFO field

[Will C]

I get this error below a lot, and it then displays nothing on the track. Other programs like Annovar skip this problem and report variants. Is there a way that IGV can accommodate this soft error and still display track? I think it would take me a long time to manually edit out the whitespace in this whole genome file. (using IGV version 2.3.40)

Error loading features for interval: chr11:88909039-89030927
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 14082: The VCF specification does not allow for whitespace in the INFO field. Offending field value was "VARTYPE_SNV;hgmd_alleles=G/A;hgmd_id=CM002936;hgmd_disease=Papillon-Lefevre syndrome;hgmd_gene=CTSC;AA=G;EUR_AF=0.85;AMR_AF=0.91;AF=0.91;AFR_AF=0.91;ASN_AF=1.00;CSQ=G|ENSG00000109861|ENST00000393302|Transcript|non_synonymous_codon|407|407|136|I/T|aTa/aCa||benign(0)|tolerated(0.61)||CTSC|||||neutral(0.004),G|ENSG00000109861|ENST00000527018|Transcript|non_synonymous_codon|328|329|110|I/T|aTa/aCa||benign(0)|tolerated(0.64)||CTSC|||||neutral(0.003),G|ENSG00000109861|ENST00000227266|Transcript|non_synonymous_codon|573|458|153|I/T|aTa/aCa||benign(0)|tolerated(0.65)|YES|CTSC|||||neutral(0.003),G|ENSG00000109861|ENST00000533865|Transcript|nc_transcript_variant|480|||||||||CTSC|||||", for input source: /Users/williamcassano/Desktop/BRIAN GENOMICS/Variations/PG0000652-BLD.snps.vcf.gz

-Will

[Jim Robinson]

Try updating to the latest igv,  it has a new version of the htsjdk.

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[Will C]

I get the same message with IGV 2.3.59 app version for Mac that I just downloaded.

[Jim Robinson]

We use the htsjdk for VCF parsing and its rather strict on the spec.
I'm not sure what can be done, but if you can prepare a small example
file with the problem I'll see if I can create a workaround. This
might also be a topic to raise on the htsjdk forum.

Jim

[Will C]

Looks like spaces appear in disease names instead of underscores or dashes. This file was created by Casava in Fall 2012 (says it's VCFv4.1) and worked fine with IGV back then. Is the no whitespace rule a recent addition? Maybe I should just convert every space character to an underscore character.

[Jim Robinson]

Hi Will,

We use the htsjdk (https://samtools.github.io/htsjdk/) for parsing
VCF, so I really can't tell you if this is a recent change or not.
You could ask on their mailing list, include a few lines of the stack
trace and/or the error message.

Jim