Read Mapping parameters
You can adjust the following read mapping parameters to optimize your analysis results when you create or edit analysis workflows.
IMPORTANT! Use the default parameter settings unless you are an advanced user.
Variant Name | Description |
|---|---|
Main tab | |
Tmap Mapped Files Enable Re-map | Flag to indicate whether mapped BAM files should be remapped. Allowed values: True or False |
Advanced tab | |
Mismatch Penalty | Specifies the mismatch penalty. Allowed values: 1 to 100 |
Soft Clipping Type | Specifies the type of soft-clipping to perform. Allowed values: 0 to 3 |
Gap Open Penalty | Specifies the gap open penalty. Allowed values: 1 to 100 |
Match Score | Specifies the match score. Allowed values: 1 to 100 |
Gap Extension Penalty | Specifies the gap extension penalty. Allowed values: 1 to 100 |
Context | Realign with context-dependent gap scores. Allowed values: True or False |
Maximum Amplicon Overrun Large INDEL Rescue | The maximum number of bases allowed for a read to overrun the end of the amplicon. Allowed values: 0 to unlimited |
Flow Score Penalty | Specifies the flow score penalty. Allowed values: 1 to 100 |
Max adapter bases for soft clipping | Specifies to perform 3' soft-clipping (via -g) if at most this # of adapter bases were found. Allowed values: 0 to unlimited |
Local Band Width | Specifies the Local band width. Allowed values: 1 to 100 |
Do Repeat Clip | Trim repetitive sequence at the ends of alignment. Allowed values: True or False |
End Repair | Specifies to perform 3' end repair. Allowed values: 0 to unlimited |
Use BED file | Use bed file to capture INDELs near amplicon edges. Allowed values: True or False |
Output Filter | Specifies the output filter for the mapping. Allowed values: 0 to 3 |
Maximum INDEL Size to Rescue | The maximum INDEL size to rescue with one large INDEL algorithm. Allowed values: 0 to unlimited |