Setting | Description |
|---|---|
Simple Mutation percentage from | Select this option to set a single mutation percentage range for all variant types, and then specify the range. Note: Applicable only for setting a range of values with a minimum value that are greater than or equal to the value that specified in the Project Wizard. See Mutation percentage <=. |
Matrix | Select this option to set independent thresholds for each variant type. Note: Applicable only if setting a value that is greater than or equal to the value that you specified in the Project Wizard. See Mutation Filter settings. |
Mutation percentage | For the indicated variation type (SNP, Indel, or Homopolymer Indel), a variation between the aligned reads and the reference sequence at a given position of the reference must occur at a frequency that exceeds this value, or a variant is not called at the position. |
SNP allele count | For the indicated variation type (SNP, Indel, or Homopolymer Indel), the total number of reads with the variant allele must exceed this value, or a variant is not called at the position. |
Total coverage count | For the indicated variation type (SNP, Indel, or Homopolymer Indel), the total number of reads at a given position must exceed this value, or a variant is not called at the position. |
Ratio of homopolymer length change | Ratio = |(ref homopolymer length –alt homopolymer length)|/ref homopolymer length. If there are multiple alt lengths, then the ratio is calculated for each alt and the largest ratio value is used. |