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

Suggested trial value: False

Tmap Realignment Enable Flag

Flag to indicate whether BAM Realignment should be invoked.

Allowed values: True or False

Suggested trial value: False

Advanced tab

Mismatch Penalty

Specifies the mismatch penalty.

Allowed values: 1 to 100

Suggested trial value: 3

Soft Clipping Type

Specifies the type of soft-clipping to perform.

Allowed values: 0 to 3

Suggested trial value: 2

Gap Open Penalty

Specifies the gap open penalty.

Allowed values: 1 to 100

Suggested trial value: 5

Match Score

Specifies the match score.

Allowed values: 1 to 100

Suggested trial value: 1

Gap Extension Penalty

Specifies the gap extension penalty.

Allowed values: 1 to 100

Suggested trial value: 2

Context

Realign with context-dependent gap scores.

Allowed values: True or False

Suggested trial value: 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

Suggested trial value: 6

Flow Score Penalty

Specifies the flow score penalty.

Allowed values: 1 to 100

Suggested trial value: 2

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

Suggested trial value: 2147483647

Local Band Width

Specifies the Local band width.

Allowed values: 1 to 100

Suggested trial value: 50

Do Repeat Clip

Trim repetitive sequence at the ends of alignment.

Allowed values: True or False

Suggested trial value: False

End Repair

Specifies to perform 3' end repair.

Allowed values: 0 to unlimited

Suggested trial value: 0

Use BED file

Use bed file to capture INDELs near amplicon edges.

Allowed values: True or False

Suggested trial value: False

Output Filter

Specifies the output filter for the mapping.

Allowed values: 0 to 3

Suggested trial value: 1

Maximum INDEL Size to Rescue

The maximum INDEL size to rescue with one large INDEL algorithm.

Allowed values: 0 to unlimited

Suggested trial value: 30