The gamtools select tool is used to select or exclude samples from a segregation table.

Usage and option summary


gamtools select [OPTIONS] -s <SEGREGATION_FILE> -o <OUTPUT_FILE>
                          -n [<SAMPLE_NAME> [<SAMPLE_NAME> ...]]

Required parameters:

Option Description
-s, –segregation-file A file containing the segregation of all samples
-n, –sample-names Names of the samples to remove
-o, –output-file Output file path (or - to write to stdout)

Optional parameters:

Option Description
-d, –drop-samples Discard the listed samples (default: discard samples not in the list)