I’m pretty new to galaxy and I’ve been working filtering a VCF file into a selection of variants that is more specified, as I am getting quite a lot of variants right now with the generic filtering. I’ve tried using vcf annotate to apply min depth and max depth, but it doesn’t seem to be working. I might have the format wrong but I’m not really sure how to properly write it so the program can recognize the filter of min(DP)>20. Any help would be great. Also, if there is a better program for filtering variants that keeps the file in vcf format I would love to hear. Thank you!
You can filter a VCF with this tool: VCFfilter.
This is the link Galaxy to the tool at UseGalaxy.org. Search the tool panel at other servers with the tool name to find it.
This tool happens to have a pretty detailed Help section, plus a link to a tutorial.
In short: the annotation you are filtering on should be declared in the header, and also present in the data lines. VCF format can vary … so always double check in those two places in your specific file to make sure the data you want to filter on exists already, then review the tool Help, to get the syntax correct.
For a DP filter, that tool should work fine. The default query is one example.
Hope that helps!