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:
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?
Saket ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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