Question: How to normalize and decompose a VCF file using only Galaxy-available tools?
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gravatar for msprindzhuk
19 months ago by
msprindzhuk50
msprindzhuk50 wrote:

How to normalize and decompose a VCF file using only Galaxy-available tools? The goal is to make it digestable for SNPEff. Without preprocessing, VCF files produced by Pilon, FreeBayes and other software do not go into the SNPEff with a frame zero error. Does anybody know how to preprocess VCFs in Galaxy?

vcf normalization • 706 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by msprindzhuk50
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gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This tutorial has examples for Freebayes -> SnpEff: https://galaxyproject.org/tutorials/var_dip/#generating-and-post-processing-freebayes-calls. Hopefully it will help with parameter settings and the like to make the data processing work out better for you.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson25k
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