This PR adds the parameter minmapq to the pileup.sh script. The atlas config parameter used is named minimum_map_quality and was added to the default config with the value of 0. This means that from the user perspective nothing has changed in the default behaviour of atlas, however the map quality can now easily be adjusted via the config file.
SilasK
commented
1 year ago
This PR adds the parameter
minmapqto thepileup.shscript. The atlas config parameter used is namedminimum_map_qualityand was added to the default config with the value of0. This means that from the user perspective nothing has changed in the default behaviour of atlas, however the map quality can now easily be adjusted via the config file.