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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

TagStandard of metricDescription
LClcr > 0Low coverage in track
LVF\( vafr\ge 1-{thr}_{vaf}^{\ast } \)Low variant allele frequency
LM(lm ≥ 0.2)  (dl ≥ 2)Low mapping quality
MMmm ≥ 1Too many mismatches around variant
HDRhdr ≥ 1The variant is supported by reads that have other recurrent mismatches
HEnh ≥ 0.9Near head
ENne ≥ 0.9Near end
NIni ≥ 0.9Near insertion
NDnd ≥ 0.9Near deletion
Ddir ≥ 0.9Almost supported reads with the same direction
SSEsse ≥ 0.9Almost supported reads with the same start and end
MV(mv ≥ 0.2)  (dmv ≥ 2)Variant locus has read support for different alleles
RRr = 1Near repeat region
RIri = 1Insertion and near repeat region and insert nucleotides are the same as minimum repeat units of reference
AOli = 1Big insertion and insert nucleotide are the same as the reference
SIsi ≥ 0.9Supported reads are short insert
(NCN)lncr = 1No coverage in normal track
(LCN)1 > lncr > 0Low coverage in normal track
(VN)(nvaf ≥ 0.1 × thr)  (dnormal ≥ 2)Variant occur in normal track
  1. thrvaf is the requirement for minimal variant allele frequency set by users. The tags in brackets are used for somatic variants