TMAP map1 options
The TMAP map1 module implements BWA-short reads mapping and has these characteristics:
-
map1 is very fast at finding perfect matches.
-
map1 is very slow at finding a set of matches with up to two mismatches.
The map1 module is not the default for TMAP, map4 is the default.
The following options are supported with the TMAP map1 module (all are optional).
|
Option |
Type |
Default |
Description |
|---|---|---|---|
|
Integer |
32 |
The k-mer length to seed CALs. -1 to disable. |
|
|
Integer |
2 |
The maximum number of edits in the seed. |
|
|
Integer |
48 |
The secondary seed length. -1 to disable |
|
|
Float |
0.04 |
The maximum number of edits or false-negative probability assuming the maximum error rate. |
|
|
Float |
0.02 |
The assumed per-base maximum error rate. |
|
|
Integer |
3 |
The maximum number of or (read length) fraction of mismatches. |
|
|
Integer |
1 |
The maximum number of or (read length) fraction of INDEL starts. |
|
|
Integer |
6 |
The maximum number of or (read length) fraction of INDEL extensions. |
|
|
Integer |
10 |
The maximum number of CALs to extend a deletion. |
|
|
Integer |
5 |
The number of bps from the end of the read. |
|
|
Integer |
32 |
Optimal CALs have been found. |
|
|
Integer |
2000000 |
The maximum number of alignment nodes. |
|
|
Integer |
-1 |
The minimum sequence length to examine. -1 to disable |
|
|
Integer |
-1 |
The maximum sequence length to examine. -1 to disable |