-excl-samplesoptions can be used to select a subset of samples to process. E.g.:
samples.txt(which should contain a whitespace-separated list of identifiers). Samples are identified by the first identifier field (often
ID_1) in the sample file, or if no sample file is specified, by sample identifiers specified in genotype data source (e.g. by the header in vcf or bgen formats). The option
-incl-samplesbehaves similarly but includes only samples with identifier in the given file.
You can currently filter sample file column values
for equality (using
==) or inequality (
Note: depending on the column names and expression used, it may be necessary
to place quotation marks around the expression to stop it being expanded by the shell.
As in the example above this also allows you to use whitespace to format the condition.
-incl-samples-where behaves similarly, but includes only samples matching the condition.
-excl-<option>. If multiple overlapping conditions are specified, the logic is that samples that satisfy any of the specified exclusion criteria will be excluded, and likewise samples that do not satisfy any of the specified inclusion criteria will be excluded. This in the following command: