For a quick breakdown of a variant pipeline, this recent workshop has
slides. Basically you map (BWA is a good choice), choose a variant
caller (Freebayes or other), and look at associated annotation (
Tools in the group "NGS: QC and manipulation" such as FastQC should be
able to help with quality checks and then others in same group with
manipulations. For the detailed steps of sorting out known SNPs,
synomymous vs non-synonymous, etc, you have a few choices. The tools
the groups ' NGS: GATK Tools (beta)', ' Phenotype Association', and
'Genome Diversity' are the places to look. Tools have help on the
including links to publications. Or you can look in the tool shed for
more choices to use in your local instance:
If the data in the shared link is really patient data that is
sensitive, I would recommend unsharing the history and deleting the
permanently from the public Main Galaxy instance.
Good luck with your thesis!
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