Bamstats parameters
You can adjust the following Bamstats parameters when you create or edit Ion Reporter™ Software analysis workflows to optimize the quality of the BAM results file that is generated during analysis.
IMPORTANT! Use the default parameter settings unless you are an advanced user.
|
Parameter name |
Description |
|---|---|
|
Main tab |
|
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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 |
|
Maximum read length |
The maximum read length.
Allowed values: 700 to 20,000 |
|
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 |
|
Max mismatches |
The maximum number of mismatches allowed in the alignments. Any alignment with more than the specified number of mismatches are ignored when reports that are related to the number of mismatches are generated. Allowed values: 0 to 500 |
|
Max base qv |
The maximum base quality values. Any base with a base quality value of more than the specified value are ignored when reports are generated. Allowed values: 0 to 100 |
|
Maximum Medium Coverage (QC) |
The maximum medium coverage value. Any base with a coverage value of more than the specified value are ignored when reports are generated. The value of Maximum Medium Coverage (QC) should be greater than Maximum Low Coverage (QC).
Allowed values: 2 to unlimited |
|
Minimum Target Overlap Forward |
The fraction of an alignment that must be overlapped by a target to be classified as on target. Allowed values: 0.000001 to 1 |
|
Maximum Low Coverage (QC) |
The maximum low coverage value. Any base with a coverage value of more than the specified value is ignored when reports are generated. Value of Maximum Low Coverage (QC) should be less than Maximum Medium Coverage (QC). Allowed values: 1 to unlimited |
|
Maximum Target Overlap Reverse |
The fraction of an alignment that must be overlapped by a target to be classified as on target. Allowed values: 0.0001 to 1 |