Without the comma, the PLINK 1.9 command line parser would interpret - failed as another flag. If the first entry in the filter description is a negative match, you now must precede the '-' with a comma, e.g. Keeps variants with the ' exonic' attribute which also lack the ' failed' and ' candidate' attributes. attrib snps.txt exonic,-failed,-candidate (When there are multiple negative match conditions, PLINK 1.9 builds before incorrectly required only one attribute to be missing.) As mentioned above, the boolean condition description is expected to be in the form of a comma-delimited list entries starting with '-' are added to the n i attribute name list ("negative match conditions"), and the rest join the p i list ("positive match conditions"). Where if there are no p i's, the first predicate is true, and if there are no n i's, the second predicate is true. attrib-indiv expects an attribute file which starts with FID and IID columns instead of a variant ID column, and filters samples instead of variants. (Variant IDs are not allowed to appear multiple times.) See on the resources page for an example. The attribute file is expected to have variant IDs in the first column of each line, followed by zero or more space-separated attribute names applying to the variant. Given a (possibly gzipped) file assigning attributes to variants, and a comma-delimited list ( with no whitespace) describing a boolean condition on the attributes, -attrib excludes all variants which are either missing from the attribute file or don't satisfy the condition. If variants have been assigned to sets (via -set/-make-set), -gene takes a space-delimited sequence of set names on the command line and removes all variants not in one of the named sets, while -gene-all only removes variants which aren't in any set (this used to happen automatically in some situations). Similarly, -remove-clusters removes all samples in clusters named in a file, and -remove-cluster-names removes all samples in clusters named on the command line. keep-clusters accepts a text file with one cluster name per line, and -keep-cluster-names takes a space-delimited sequence of cluster names on the command line. If samples are assigned to clusters (via -within/-family), -keep-clusters and -keep-cluster-names can be used individually or in combination to define a list of clusters to keep all samples not in one of those clusters are then removed from the current analysis. If your intention is to resolve duplicates, you should now use -bmerge instead of -exclude. Note that this is slightly different from PLINK 1.07's behavior when the main input fileset contains duplicate variant IDs: PLINK 1.9 removes all matches, while PLINK 1.07 just removes one of the matching variants. exclude does the same for all listed variants. With the ' range' modifier, the input file should be in set range format instead. extract normally accepts a text file with a list of 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. When operating on multiple ID lists, you may want to use these flags in conjunction with Unix text manipulation utilities (e.g. Similarly, -keep-fam and -remove-fam accept text files with family IDs in the first column, and keep or remove entire families. remove does the same for all listed samples. keep accepts a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column, and removes all unlisted samples from the current analysis. If variation is problematic, use -freqx to export initial statistics, and then include -read-freq in all filtering passes where you want to refer back to the initial statistics. Some of these criteria are based on statistics such as estimated MAF that may vary through multiple filtering passes. 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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