TMAP map1 Options

This page describes the parameters for the TMAP map1 module. The map1 module implements BWA-short reads mapping and has these characteristics:

Note:

The map1 module is not the current default for TMAP.

Options supported with the TMAP map1 module (all are optional):

--seed-length	INT	32	The k-mer length to seed CALs (-1 to disable)
--seed-max-diff	INT	2	The maximum number of edits in the seed
--seed2-length	INT	48	The secondary seed length (-1 to disable)
--max-diff	NUM	0.04	The maximum number of edits or false-negative probability assuming the maximum error rate
--max-error-rate	FLOAT	0.02	The assumed per-base maximum error rate
--max-mismatches	NUM	3	The maximum number of or (read length) fraction of mismatches
--max-gap-opens	NUM	1	The maximum number of or (read length) fraction of indel starts
--max-gap-extensions	NUM	6	The maximum number of or (read length) fraction of indel extensions
--max-cals-deletion	INT	10	The maximum number of CALs to extend a deletion
--indel-ends-bound	INT	5	The number of bps from the end of the read
--max-best-cals	INT	32	Optimal CALs have been found
--max-nodes	INT	2000000	The maximum number of alignment nodes
--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)
Option	Type	Default	Description