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Question: How to normalize and decompose a VCF file using only Galaxy-available tools?
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20 months ago by
msprindzhuk • 50
msprindzhuk • 50 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 • 754 views
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modified 20 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by msprindzhuk • 50
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20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
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