Bamstats parameters

You can adjust the following Bamstats parameters to optimize your analysis results when you create or edit Ion Reporter™ Software analysis workflows.

IMPORTANT! Use the default parameter settings unless you are an advanced user.

Parameter name

Description

Main tab

Maximum Coverage

The maximum coverage of locations in the reference. Locations with coverage more than the maximum coverage values are ignored during coverage calculations.

Allowed values: 100 to 1,000,000

Suggested trial value: 100,000

Maximum read length

The maximum read length.

Allowed values: 700 to 20,000

Suggested trial value: 700

Advanced tab

Max mapping qv

The maximum mapping quality value. Any alignment with mapping quality value more than the specified value is ignored.

Allowed values: 0 to 255

Suggested trial value: 255

Max mismatches

The maximum number of mismatches allowed in the alignments. Any alignment with more then the specified number of mismatches are ignored while generating reports related to the number of mismatches.

Allowed values: 0 to 500

Suggested trial value: 500

Max base qv

The maximum base quality values. Any base with a base quality value of more then the specified value are ignored while generating reports.

Allowed values: 0 to 100

Suggested trial value: 100

Maximum Medium Coverage (QC)

The maximum medium coverage value. Any base with a coverage value of more then the specified value are ignored while generating reports. The value of Maximum Medium Coverage (QC) should be greater than Maximum Low Coverage (QC).

Allowed values: 2 to unlimited

Suggested trial value: 1,000

Minimum Target Overlap Forward

The fraction of an alignment that must be overlapped by a target in order to be classified as on target.

Allowed values: 0.000001 to 1

Suggested trial value: 0.000001

Maximum Low Coverage (QC)

The maximum low coverage value. Any base with a coverage value of more then the specified value is ignored while generating reports. Value of Maximum Low Coverage (QC) should be less than Maximum Medium Coverage (QC).

Allowed values: 1 to unlimited

Suggested trial value: 500

Maximum Target Overlap Reverse

The fraction of an alignment that must be overlapped by a target in order to be classified as on target.

Allowed values: 0.0001 to 1

Suggested trial value: 0.5