Table 1 Description of tags used to annotate variants and the standards of corresponding metrics
From: VariFAST: a variant filter by automated scoring based on tagged-signatures
Tag | Standard of metric | Description |
|---|---|---|
LC | lcr > 0 | Low coverage in track |
LVF | \( vafr\ge 1-{thr}_{vaf}^{\ast } \) | Low variant allele frequency |
LM | (lm ≥ 0.2) ∧ (dl ≥ 2) | Low mapping quality |
MM | mm ≥ 1 | Too many mismatches around variant |
HDR | hdr ≥ 1 | The variant is supported by reads that have other recurrent mismatches |
HE | nh ≥ 0.9 | Near head |
EN | ne ≥ 0.9 | Near end |
NI | ni ≥ 0.9 | Near insertion |
ND | nd ≥ 0.9 | Near deletion |
D | dir ≥ 0.9 | Almost supported reads with the same direction |
SSE | sse ≥ 0.9 | Almost supported reads with the same start and end |
MV | (mv ≥ 0.2) ∧ (dmv ≥ 2) | Variant locus has read support for different alleles |
RR | r = 1 | Near repeat region |
RI | ri = 1 | Insertion and near repeat region and insert nucleotides are the same as minimum repeat units of reference |
AO | li = 1 | Big insertion and insert nucleotide are the same as the reference |
SI | si ≥ 0.9 | Supported reads are short insert |
(NCN) | lncr = 1 | No coverage in normal track |
(LCN) | 1 > lncr > 0 | Low coverage in normal track |
(VN) | (nvaf ≥ 0.1 × thr) ∧ (dnormal ≥ 2) | Variant occur in normal track |