Setting | Description |
|---|---|
Use original | Applicable only when aligning condensed reads. If this option is selected, then the mutation percentage refers to the original read numbers and not the condensed read numbers. A variation that is detected must exceed the specified percentage of original reads for it to be reported as a variant. Reads that align to the position that is at the end of the read (outside of the anchor and shoulder sequences) are not included in the count of aligned reads. Note: This option is useful for eliminating false positives. |
Except for homozygous | Selected by default. The coverage requirement is ignored for variants that are homozygous. |
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. |
Note: The values for the mutation percentage, the SNP allele count, and the total coverage count must be met for an indicated variation type at a given position to be reported as a variant. If any criterion is not met, then the variation is filtered from the analysis and it is highlighted in gray in the Alignment viewer. | |
Perform in-read phasing | Selected by default. Strings of variants that are within a user-defined proximity (0 -3 bp) and are on the same reads are merged into a single indel call. |
Max Gap between two variants | The maximum number of bp allowed between variants on the same strand to be merged into a single indel call (phased). If the number of bp exceeds this threshold, then the variants are not phased. |
Phaseable reads percentage | The minimum percentage of reads in the phased region that must have at least one of the phaseable variants for the phasing to include the variant position. |