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 LDBIRD to only focus on the specified variants, and an exclusion variant (-excl-...) which tells LDBIRD to ignore the specified variants, and each applies either to the predictor or outcome genotypes:

• -g1-[in|ex]cl-range: specify a genomic range or list of ranges to include or exclude outcome variants from, applied to the file specified by -g1.

• -g1-[in|ex]cl-rsids: specify a set of variant IDs to include or exclude outcome variants from, applied to the file specified by -g1.

• -g2-[in|ex]cl-range: as above but for the file specified by -g2.

• -g2-[in|ex]cl-rsids: as above but for the file specified by -g2.

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 named of the sample file to the given value, and include/exclude samples based on whether the values match (= or ==) or mismatch (!=).