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?
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