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View Code? Open in Web Editor NEWStarting with tsv files from MSG, pull requested individuls and thin data
Starting with tsv files from MSG, pull requested individuls and thin data
This is a little utility for post-processing .tsv files produced by the Multiplexed Shotgun Genotyping (msg) pipeline DEPENDENCIES Python 2.7 USAGE python pull_thin_tsv.0.5.1.py <config_file: default = pt.cfg> If no config_file provided, program looks for pt.cfg in same folder INFORMATION For info on msg, see github.com/JaneliaSciComp/msg This utility will perform the following tasks 1 - Pull out specific individuals from across multiple tsv files 2 - Reduce each file to thinned data (defined by parameter difffac), keeping the flanking values with values < difffac 3 - Can replace the NAs in the files with priors, which is useful for some downstream applications, such as R-QTL Known issues: 1 - Properly recognizes if *par2 files have been preprocessed, but does not recognize for *par1 files. 2 - Does not find "sex" column in phenofile for csv files, only for tab delimited files.
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