Editable parameters in the analysis configuration file

Parameter

Description

Min Read Count

This column allows users to set custom minimum read count thresholds for different targets. If the value is specified as "Use Global Value" for a target (the value in the row) in this column, then the global minimum read count threshold is used. (For example: 20 reads or 40 reads for Fusions as set using the minimum read count for Fusions parameter.) If a user changes the value for any target from "Use Global Value" to an allowed integer value (for example: 50), then that value overrides the global threshold. The new threshold (50 in this example) is used to call that target as Present/Absent. All other targets will still use the global threshold. This column overrides these global parameters at the individual target level (minimum read count for Fusions, minimum read count for Controls, minimum read count for Gene Expression, minimum read count for Non-Targeted fusions). This property is not applicable to 5p3pAssay type targets.

Min Normalized read count

This column allows users to set custom minimum normalized read count thresholds for different targets. If the value is specified as "Use Global Value" for a target (the value in the row) in this column, then the global minimum read count threshold is used. (For example : 0.0 or 0.0015 reads for Fusions.) If a user changes the value for any target from "Use Global Value" to an allowed value (for example : 0.1) , then it overrides the global threshold and the new threshold (0.1 in this example) is used to call the target as Present/Absent. This column can be used to override the minimum normalized read count global parameters at individual target. This property is not applicable to 5p3pAssay type targets.

Make Calls

This column allows users to enable making Present/Absent call for RNAExonVariants at individual target level. This property is not applicable to any other type. By default the analysis workflow parameters are set to not make calls for all the RNAExonVariants. If the value for any RNAExonVariant target (the value in the row) is changed from "Use Global value" to "True", the target will be called Present/Absent based on the read count and wild type ratio.

Min WT Ratio

This column allows users to set custom threshold for minimum wild type ratio for RNAExonVariants at individual target level.

Do Not Report

By changing the value to "True" for any target, that target is not displayed in the output files and reports.

Max Read Count Negative

This column allows users to set nocall range for any fusion target. The value specified in this column should be always less than or equal to the value for minimum read count as set by global parameter threshold or custom threshold for that target.

For example, if a global threshold for minimum read count for fusion is 40, and Max Read Count Negative is set to 20 for a target (T1)_ , if the count of target T1 is between 20 and 40, it will be called as nocall. If the count is <20, it is called as absent; if it is >40 it is called as present.

This is not applicable to 5p3pAssay type targets.

If the value for Max Read count Negative is equal to the min read count for any target, then the target is called Absent; if the read count is less than that value, it is called as Present.

Minimum Imbalance Score for the RNAExon Tile Assays

Minimum imbalance score for calling 'imbalance positive' from RNA exon tiling assays in a driver gene. Positive calls also depend on p-value for imbalance.

Maximum p-value for Imbalance for the RNAExon Tile Assays

Maximum statistical significance p-value for calling 'imbalance positive' from RNA exon tiling in a driver gene. Positive calls also depend on imbalance scores.

Minimum average read counts from all the Exon Tiling assays in a Driver Gene to proceed with Imbalance

Mean coverage of a driver gene with RNA exon tiling assays. Measured per gene, as the total valid mapped reads counts from all exon-tiling assays divided by the number of exon-tiling assays.