If a fourth 'skip' parameter is provided to -extract-col-cond, it is interpreted as a number of initial lines to skip if it's a number otherwise it must be a single (possibly quoted) character, and all lines starting with that character are skipped.These column numbers can be changed by providing additional parameters to -extract-col-cond. By default, values are read from column 2 of the file, and variant IDs are read from column 1.(This is a generalization of PLINK 1.x's -qual-scores flag.) It is designed to support filtering on INFO-like values stored in a separate tab-delimited file. extract-col-cond excludes all variants which either don't appear in the given input file, or are associated with a value which doesn't satisfy the given condition.
bed-border-kb interprets its argument as a kilobase count, and is otherwise identical. "-extract bed0") by the given number of base-pairs on both sides.
bed-border-bp extends all the intervals in an input BED file (for e.g. extract-intersect is just like -extract, except that a variant must be in the intersection, rather than just the union, of the -extract-intersect files to be kept. exclude does the same for all listed variants. For backward compatibility, ' range' is an alias for 'bed1'. With the ' bed0' or ' bed1' modifier, the input file should be in 0-based or 1-based interval-BED format instead. extract normally accepts one or more text file(s) with variant IDs (usually one per line, but it's okay for them to just be separated by spaces), and removes all unlisted variants from the current analysis. indv accepts a single 1-3 part sample ID, and removes all samples with different IDs. If there is no header line, one-column lines are treated as IIDs, and multicolumn lines are treated the same way as in PLINK 1.x (first two columns assumed to be FID/IID).(Note that when FID is undefined, it is treated as '0'.) As long as the first columns are "#FID IID", "#FID IID SID", "#IID", or "#IID SID", PLINK 2 will do the right thing. If the first line starts with '#FID' or '#IID', it will be treated as a header line.keep/-remove now support a wider variety of sample ID file formats: Similarly, -keep-fam and -remove-fam accept text files with family IDs in the first column, and keep or remove entire families.
keep accepts one or more space/tab-delimited text files with sample IDs, and removes all unlisted samples from the current analysis -remove does the same for all listed samples. If variation is problematic, use " -freq counts" to export initial statistics, and then include -read-freq in all filtering passes where you want to refer back to the initial stats. Some of these criteria are based on statistics such as estimated MAF that may vary through multiple filtering passes.When a filter type can apply to either samples or variants, the sample-filter flag names start with 'keep'/'remove', and the variant-filter flag names start with 'extract'/'exclude'.The following flags allow you to exclude samples and/or variants from an analysis batch based on a variety of criteria.
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