faFilter [options] in.fa out.fa


This tool is part of UCSC Genome Browser's utilities.

-name=wildCard - Only pass records where name matches wildcard
* matches any string or no character.
? matches any single character.
anything else etc must match the character exactly
(these will will need to be quoted for the shell)
-namePatList=filename - A list of regular expressions, one per line, that
will be applied to the fasta name the same as -name
-v - invert match, select non-matching records.
-minSize=N - Only pass sequences at least this big.
-maxSize=N - Only pass sequences this size or smaller.
-maxN=N Only pass sequences with fewer than this number of N's
-uniq - Removes duplicate sequence ids, keeping the first.
-i - make -uniq ignore case so sequence IDs ABC and abc count as dupes.

All specified conditions must pass to pass a sequence. If no conditions are
specified, all records will be passed.

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