Rastair's output follows the VCFv4.5 specification.
| Name | Description |
|---|
PASS | All filters pass |
lowDp | Low read depth |
dnCpG_lowDp | Low read depth for de-novo CpG candidate |
dnCpG_bq | Low base quality for de-novo CpG candidate |
dnCpG_mapq | Low mapping quality for de-novo CpG candidate |
dnCpG_vaf | Low variant allele frequency for de-novo CpG candidate |
dnCpG_adj | Included as adjacent position for de-novo CpG candidate, but other position did not pass filters |
m_vaf | Low variant allele frequency for methylation candidate |
m_bq_ratio | Low quality ratio for methylation candidate |
m_pos | Alt allele evidence from read edges for methylation candidate |
m_highDp | Excessive coverage for methylation candidate |
pre_ml | Low amount of usable evidence, skipping ML |
low_ml_score | Machine Learning module prediction below threshold |
| Name | Description | VCF Type | Rust Type | Occurance |
|---|
AD | Total read depth for each allele | Integer | usize | R |
BQ | RMS base quality | Float | RootMeanSquare | 1 |
DP | Combined depth across samples | Integer | usize | 1 |
MQ | RMS mapping quality | Float | RootMeanSquare | 1 |
MQ0 | Number of MAPQ == 0 reads | Integer | usize | 1 |
NS | Number of samples with data | Integer | usize | 1 |
AS_SB_OT | OT counts per allele | Integer | u32 | R |
AS_SB_OB | OB counts per allele | Integer | u32 | R |
SC5 | 5-base sequence context centered on the variant position | String | SmolStr | 1 |
AF | Allele frequency for each ALT allele in the same order as listed (estimated from primary data, not called genotypes) | Float | f64 | A |
ABQ | RMS Base quality per allele | Float | f64 | R |
AMQ | RMS Map quality per allele | Float | f64 | R |
AS_SS_BQ_OT | Strand-specific RMS of base quality per allele on the original top strand | Float | f32 | R |
AS_SS_BQ_OB | Strand-specific RMS of base quality per allele on the original bottom strand | Float | f32 | R |
AS_SS_MQ_OT | Strand-specific RMS of mapping quality per allele on the original top strand | Float | f32 | R |
AS_SS_MQ_OB | Strand-specific RMS of mapping quality per allele on the original bottom strand | Float | f32 | R |
PIR | RMS of relative position in read | Float | f64 | R |
ENT100 | Shannon entropy of 100bp sequence context around variant position. Value range (0..2) | Float | f64 | 1 |
NAB | RMS of number of aligned bases | Float | f64 | R |
NOI | RMS of number of indels | Float | f64 | R |
M5mC_Strands | Number of reads that are evidence for unmodified, modified, no SNP, snp | Integer | u32 | 4 |
CPG | Is this a CpG site? | Flag | bool | 0 |
CPGnovo | De-novo CPG candidate: Could the alt alleles create a new CpG site? | Flag | bool | 0 |
| Name | Description | VCF Type | Rust Type | Occurance |
|---|
GT | Genotype | String | GenotypeAllele | 1 |
GL | Genotype likelihoods, Phred-scaled | Integer | Phred> | G |
GC | Genotype confidence, Phred-scaled | Integer | Phred> | G |
DP | Read depth | Integer | usize | 1 |
M5mC | Methylation level at CpG sites | Float | Option<f64> | M |
ML | Prediction of methylation/variant likelihood by rastair's machine learning model | Float | f64 | A |