TMAP map4 Options

This page describes the parameters for the TMAP map4 module. The map4 module is based on the BWA fastmap routine and searches for the maximum exact matches between the reads and reference.

Note:

The map4 module is the current default for TMAP.

Options supported with the TMAP map4 module (all are optional):

Option	Type	Default	Description
--context	--	off	Modifies the gap penalty in homopolymers to achieve more accurate alignments
--do-repeat-clip	--	off	Clips repetitive sequence ends of aligned reads
--hit-frac	FLOAT	0.2	The fraction of seed positions that are under the maximum
--end-repair	INT	0	Rescues false negatives by selectively forcing alignment at the 3' end of the read. The recommended value is 15.
--J	INT	off 2147483647	Rescues false negatives by selectively forcing alignment at the 3' end of the read. The recommended value is 25.
--seed-step	INT	8	The number of bases to increase the seed for each seed increase iteration (-1 to disable)
--min-seed-length	INT	-1	The minimum seed length to accept hits (-1 to disable)
--max-seed-length	INT	48	The maximum seed length to accept hits
--max-seed-length-adj-coef (-1 to disable)	FLOAT	2.0	maximum seed length adjustment coefficient (-1 to disable)
--max-iwidth	INT	20	The maximum interval size to accept a hit
--max-repr	INT	3	The maximum representative hits for repetitive hits
--rand-repr	INT	false	Choose the representative hits randomly. Otherwise uniformly
--use-min	Boolean	false	When seed stepping, try seeding when at least the minimum seed length is present. Otherwise, use the maximum seed length.
--min-seq-length	INT	-1	The minimum sequence length to examine (-1 to disable)
--max-seq-length	INT	-1	The maximum sequence length to examine (-1 to disable)