This is due to a mismatch is chromosome names between your hg19.len file (UCSC naming) and the VCF (Ensembl naming). This should be handled better by Galaxy, and I’ve created a card for it: https://trello.com/c/bjmNesZj In the meantime, I used this command to convert chromosome names for this VCF: sed -E 's/^[0-9XY]+/chr&/‘ input.vcf | sed -E 's/^MT/chrM/' You may need to massage it depending on your platform and sed version. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 20, 2014, at 11:27 AM, Saket Choudhary <saketkc@gmail.com> wrote:

I am trying to visualise VCF exported from: ftp://ngs.sanger.ac.uk/production/cosmic/CosmicCodingMuts_v68.vcf.gz

However I get the following error: (Both on Galaxy Main and Local installation)

Input error: Chromosome 1 found in your input file but not in your genome file. needLargeMem: trying to allocate 0 bytes (limit: 100000000000)

The input file seems to be conforming to VCF4.1 format. Is this an issue with trackster instead?

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