Question: How to normalize and decompose a VCF file using only Galaxy-available tools?
0
gravatar for msprindzhuk
16 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 • 554 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by msprindzhuk50
0
gravatar for Jennifer Hillman Jackson
16 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 16 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 91 users visited in the last hour