Pruning big files - Filtering SNPs

vcf
variant
snp
filter

#1

Hi everybody.
I’m new with Galaxy tool and I’ve a problem. I need to “prun” a big SNP file, taking the only ones that are indipendent.
I can’t find a Galaxy function that can do it. Can you please help me?

Thank you.


#2

I’m not sure what you mean by “independent” but there are many tools in Galaxy that can annotate, filter, and manipulate SNP data in vcf format.

Examples can be found by searching by the keyword vcf or snp in the tool panel of the Galaxy server you are working at (if public) or in the ToolShed (if working in your own Galaxy server and are searching for new tools).

It also might find it helpful to review Variant analysis tutorials for example tools and usage.

If those do not help, please explain more about your data source or what tool produced it, the file format, and what content you want to filter. An example would help: screenshot or a sample of the data pasted into your reply.