This pull request is aimed at facilitating data preparation for running snpArcher. It includes:
A helper script, clean_coords.R, that uses tidyverse and pazer R packages to clean up messy input lat/lon coordinates and produce a QC sample sheet that can used with snpArcher. Currently this outputs a reduced sample sheet only usable for the QC module, and it requires that your input data store coordinates either in separate columns called Latitude and Longitude, or in a single lat_lon column (these are the common SRA coord formats). It handles many messy inputs but not guaranteed to work on everything.
This pull request is aimed at facilitating data preparation for running snpArcher. It includes: