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.
Assistant Professor of Computational Biology
George Washington University
On Apr 20, 2014, at 11:27 AM, Saket Choudhary <sake...@gmail.com> wrote:
> I am trying to visualise VCF exported from:
> However I get the following error: (Both on Galaxy Main and Local
> Input error: Chromosome 1 found in your input file but not in your genome
> 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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