Table 1.
VCF fields extracted by VariantAnnotation package.
| Category | Field | Type | Description |
|---|---|---|---|
| INFO | AC | Integer | Allele count in genotypes, for each ALT allele, in the same order as listed |
| DB | Flag | dbSNP membership | |
| DP | Integer | Approximate read depth: some reads may have been filtered | |
| FS | Float | Phred-scaled p value using Fisher's exact test to detect strand bias | |
| MQ | Float | RMS mapping quality | |
| SOR | Float | Symmetric odds ratio of 2 × 2 contingency table to detect strand bias | |
|
| |||
| GENO | AD | Integer | Allelic depths for the ref and alt alleles in the order listed |
| GQ | Integer | Genotype quality | |
|
| |||
| FIXED | QUAL | Float | A quality score associated with the inference of the given alleles |