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Question: vcf filter error
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gravatar for madhavi.maddali
7 months ago by
madhavi.maddali • 0
madhavi.maddali • 0 wrote:

I am using the shared workflow -hg19-ngs-workflow-bwa-freebayes-annovar in galaxy. I have problem with vcffilter. It is giving an error "An error occurred with this dataset: Fatal error: Exit code 134 () terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 1) > this->size() (which is 0) /galaxy-repl/main/jobdir/018/982/189" Could you please help?
genome format vcf galaxy mismatch • 343 views
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modified 7 months ago • written 7 months ago by madhavi.maddali • 0
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gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The problem is likely one of these:

  1. A formatting problem with the input VCF.
  2. The VCF input is empty or only contains header lines.
  3. There was a reference genome mismatch problem during this step or prior steps. Mismatched inputs/database assignment during mapping or SNP calling can produce empty or header-only results with mismatched inputs.

Support FAQs that cover troubleshooting topics: https://galaxyproject.org/support/#troubleshooting

Galaxy Tutorials: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for madhavi.maddali
7 months ago by
madhavi.maddali • 0
madhavi.maddali • 0 wrote:

Thank you for your reply
ADD COMMENT • link written 7 months ago by madhavi.maddali • 0
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