Filtering variants
The following options can be used to filter variants from the analysis. Each of these options comes in an inclusiong
variant (-incl-...
), which tells HPTEST to only focus on the specified variants, and an exclusion variant
(-excl-...
) which tells HPTEST to ignore the specified variants, and each applies either to the predictor or outcome genotypes:
-
-[in|ex]cl-outcome-range
: specify a genomic range or list of ranges to include or exclude outcome variants from. -
-[in|ex]cl-outcome-rsids
: specify a set of variant IDs to include or exclude outcome variants from. -
-[in|ex]cl-predictor-range
: specify a genomic range or list of ranges to include or exclude predictor variants from. -
-[in|ex]cl-predictor-rsids
: specify a set of variant IDs to include or exclude predictor variants from.
Filtering samples
The following options can be used to filter samples from the analysis:
-
-[in|ex]cl-samples
: specify a list of samples to include or exclude from the analysis. For this purpose, samples are identified by their identifier in the first column of the sample file. -
-[in|ex]cl-samples-where
: specify a condition to apply to rows of the sample file to determine if the sample should be included or excluded. The general syntax is-[in|ex]cl-samples-where '<column>[=|==|!=]<value>'
, which will cause HPTEST to compare the values in the column namedof the sample file to the given value, and include/exclude samples based on whether the values match (= or ==) or mismatch (!=).