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
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
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