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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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compMUMMer usage #111

Open jeff-sc-chu opened 4 years ago

jeff-sc-chu commented 4 years ago

Hi,

compMUMMer usage is unclear. The parameters being: SVs VCF file Output of MUMMer Show-diff Allowed distance (e.g. 100bp) Output: annotated vcf file

After a few trial & error, I realized

  1. Show-diff output can't be the output directly but has to be a fofn?
  2. I'm not sure what is trying to parse for VCF files as it is looking for a file with the sample name. my command were as follows:

    SURVIVOR compMUMMer rice.vcf mummer.list 100 output.vcf File Parser: could not open file: rice

Perhaps it is looking for a very specific file structure? Any help would be appreciated.

Thanks.