Setting | Description |
|---|---|
Balance Ratios and Frequency <= | • SNPs – Eliminates variant calls that are likely false positives. If both the frequency and balance ratio values for the variant fall below the set thresholds, then the variant is filtered. |
• Indels – Selected by default. Eliminates variant calls that are likely false positives. If both the frequency and balance ratio values for the variant fall below the set thresholds, then the variant is filtered. | |
• Homopolymer Indels – Selected by default. Homopolymers are defined as the reference is > 2 bases and the reads are > 1 base. This means that CC>C is a homopolymer deletion and C>CC is not a homopolymer insertion. If both the frequency and balance ratio values for the variant fall below the set thresholds, then the variant is filtered. | |
Balance Ratio calculation - Select which balance ratio value to use for the filtering variants. You can select only one value to use for the actual filtering, but you can indicate whether to display one or both values in the Mutation report. | |
• Relative to counts | Selected by default. Show the smaller of the two ratios: • #F/#R–The ratio of the number (count) of forward reads with the variant to the number of reverse reads with the variant. • #R/#F–The ratio of the number (count) of reverse reads with the variant to the number of forward reads with the variant. |
• Relative to percentage | Show the smaller of the two ratios: • %ALTF/%ALTR–The ratio of the percentage of forward reads with the alternate allele to the percentage of reverse reads with the alternate allele. • %ALTR/%ALTF–The ratio of the percentage of reverse reads with the alternate allele to the percentage of forward reads with the alternate allele Note: This value is useful for regions that have coverage in only one direction. |
Filter 1 directional cells | Select this option to filter out variants that have overall coverage in only one direction. |