Filtered variants
Variants not passing filters are annotated with a label indicating which threshold the variant failed to meet. This section provides an overview of all possible filter labels. Note that some variants may be excluded prior to filtering and will therefore not receive a filter label or appear in the output.
Filter labels reflect the stage at which the variant failed:
- Labels prefixed with 'PRE' originate from preliminary filtering performed before haplotype generation. Variants failing at this stage will only have the annotation used for the failed threshold; other annotations are not computed.
- Labels without a prefix originate from filtering performed after haplotype generation. Variants failing at this stage will have all annotations.
Each variant is assigned at most one filter label.
- Preliminary filtering labels
- PRE_PVALUE_GLOBAL: Variant failed significance threshold using global error rate. See 'Filter' under Somatic variant detection for details on early exclusion based on p-value.
- PRE_HOMOPOLYMER_FILTER: Variant discarded in homopolymer filter.
- PRE_STR_FILTER: Variant discarded in STR filter.
- PRE_STRAND_BALANCE: Variant failed strand balance threshold.
- PRE_PVALUE_LOCAL: Variant failed significance threshold using local error rate.
- PRE_COUNT_FWD: Variant failed minimum forward read count threshold.
- PRE_COUNT_REV: Variant failed minimum reverse read count threshold.
- PRE_COUNT: Variant failed minimum read count threshold.
- PRE_NOISY_SITE: Variant present at a noisy site and the expected counts have therefore been adjusted to reflect this. The resulting adjusted p-value - global error rate failed the significance threshold.
- Post-haplotype filtering labels
- AVG_Q: Variant failed minimum average quality threshold.
- COUNT: Variant failed minimum read count threshold.
- MAPPING_Q: Variant failed minimum average mapping quality threshold.
- MAPPING_Q_RATIO: Variant failed minimum average mapping quality ratio threshold.
- STRAND_BALANCE: Variant failed strand balance threshold.
- FREQ: Variant failed minimum frequency threshold.
- QUAL: Variant failed minimum QUAL threshold.
- PVALUE_GLOBAL: Variant failed significance threshold using global error rate. See 'Filter' under Somatic variant detection for details on early exclusion based on p-value.
- STRAND_MIN_COUNT: Variant failed minimum per-strand read count threshold.