Question: What Galaxy tools can preprocess VCF file before running the SNPEff annotation process?
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gravatar for msprindzhuk
10 months ago by
msprindzhuk40
msprindzhuk40 wrote:

What Galaxy tools can preprocess VCF file before running the SNPEff annotation process? We have tried VT Normalize. It does not help. What are the other ways to make VCF digestable to SNPEff?

ADD COMMENTlink written 10 months ago by msprindzhuk40

Snpeff should accept any properly formed vcf. There should be no need to preprocess it. Is data type = vcf? What is the problem you are having?

ADD REPLYlink written 10 months ago by Guy Reeves1.0k
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