---
name: "vcf"
section: "5"
platform: "linux"
package: "libhts3t64"
version: "1.21+ds-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf"
---

# vcf(5)

Variant Call Format

## NAME

vcf - Variant Call Format

## DESCRIPTION

The Variant Call Format (VCF) is a TAB-delimited format with each data line consisting of the following fields:

| | | |
| --- | --- | --- |
| 1 | **CHROM** | CHROMosome name |
| 2 | **POS** | the left-most POSition of the variant |
| 3 | **ID** | unique variant IDentifier |
| 4 | **REF** | the REFerence allele |
| 5 | **ALT** | the ALTernate allele(s) (comma-separated) |
| 6 | **QUAL** | variant/reference QUALity |
| 7 | **FILTER** | FILTERs applied |
| 8 | **INFO** | INFOrmation related to the variant (semicolon-separated) |
| 9 | **FORMAT** | FORMAT of the genotype fields (optional; colon-separated) |
| 10+ | **SAMPLE** | SAMPLE genotypes and per-sample information (optional) |

The following table gives the **INFO** tags used by samtools and bcftools.

- **AF1**

  Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele (double)

- **DP**

  Raw read depth (without quality filtering) (int)

- **DP4**

  \# high-quality reference forward bases, ref reverse, alternate for and alt rev bases (int\[4\])

- **FQ**

  Consensus quality. Positive: sample genotypes different; negative: otherwise (int)

- **MQ**

  Root-Mean-Square mapping quality of covering reads (int)

- **PC2**

  Phred probability of AF in group1 samples being larger (,smaller) than in group2 (int\[2\])

- **PCHI2**

  Posterior weighted chi^2 P-value between group1 and group2 samples (double)

- **PV4**

  P-value for strand bias, baseQ bias, mapQ bias and tail distance bias (double\[4\])

- **QCHI2**

  Phred-scaled PCHI2 (int)

- **RP**

  \# permutations yielding a smaller PCHI2 (int)

- **CLR**

  Phred log ratio of genotype likelihoods with and without the trio/pair constraint (int)

- **UGT**

  Most probable genotype configuration without the trio constraint (string)

- **CGT**

  Most probable configuration with the trio constraint (string)

- **VDB**

  Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites (float)

- **RPB**

  Mann-Whitney rank-sum test for tail distance bias (float)

- **HWE**

  Hardy-Weinberg equilibrium test (Wigginton et al) (float)

## SEE ALSO

- https://github.com/samtools/hts-specs

  The full VCF/BCF file format specification

- *A note on exact tests of Hardy-Weinberg equilibrium*

  Wigginton JE et al PMID:15789306