Pruning big files - Filtering SNPs

[jennaj]

@salvatore_d

I need to “prun” a big SNP file, taking the only ones that are indipendent.

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.

@jennaj

• Galaxy Training Network Tutorials : Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

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.