Question: When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis genome we have: WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found
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16 months ago by
msprindzhuk50
msprindzhuk50 wrote:

When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis reference built-in genome we have:

WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found. File '/home/galaxy/galaxy/database/files/000/dataset_165.dat', line 34 WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found. File '/home/galaxy/galaxy/database/files/000/dataset_165.dat'

How to debug SNPEff or what to change in the input data?

snpeff vcf vt input • 255 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by msprindzhuk50
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