Question: How to normalize and decompose a VCF file using only Galaxy-available tools?
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gravatar for msprindzhuk
10 months ago by
msprindzhuk40
msprindzhuk40 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 • 383 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson23k • written 10 months ago by msprindzhuk40
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gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson23k 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 10 months ago by Jennifer Hillman Jackson23k
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