---
name: "vcf-annotate"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf-annotate"
---

# vcf-annotate(1)

annotate VCF file, add filters or custom annotations

## NAME

vcf-annotate - annotate VCF file, add filters or custom annotations

## SYNOPSIS

**cat** *in.vcf \| vcf-annotate* \[*OPTIONS*\] *\> out.vcf*

## DESCRIPTION

About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.

-

  Currently annotates only the INFO column, but it will be extended on demand.

## OPTIONS

- **-a**, **--annotations** \<file.gz\>

  The tabix indexed file with the annotations: CHR\\tFROM\[\\tTO\]\[\\tVALUE\]+.

- **-c**, **--columns** \<list\>

  The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third column should be ignored. If TO is not present, it is assumed that TO equals to FROM.

- **-d**, **--description** \<file\|string\>

  Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. The descriptions can be read from a file, one annotation per line.

- **-f**, **--filter** \<list\>

  Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.

- **-h**, -?, **--help**

  This help message.

### Filters:

- \+

  Apply all filters with default values (can be overridden, see the example below).

- **-X**

  Exclude the filter X

- 1, StrandBias

  FLOAT                    Min P-value for strand bias (given PV4) \[0.0001\]

- 2, BaseQualBias

  FLOAT                  Min P-value for baseQ bias \[1e-100\]

- 3, MapQualBias

  FLOAT                   Min P-value for mapQ bias \[0\]

- 4, EndDistBias

  FLOAT                   Min P-value for end distance bias \[0.0001\]

- a, MinAB

  INT                           Minimum number of alternate bases \[2\]

- c, SnpCluster

  INT1,INT2                Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases \[\]

- D, MaxDP

  INT                           Maximum read depth \[10000000\]

- d, MinDP

  INT                           Minimum read depth \[2\]

- q, MinMQ

  INT                           Minimum RMS mapping quality for SNPs \[10\]

- Q, Qual

  INT                            Minimum value of the QUAL field \[10\]

- r, RefN

  Reference base is N \[\]

- W, GapWin

  INT                          Window size for filtering adjacent gaps \[10\]

- w, SnpGap

  INT                          SNP within INT bp around a gap to be filtered \[10\]

### Example:

-

  zcat in.vcf.gz \| vcf-annotate **-a** annotations.gz **-d** descriptions.txt \| bgzip **-c** \>out.vcf.gz zcat in.vcf.gz \| vcf-annotate **-f** +/-a/c=3,10/q=3/d=5/-D **-a** annotations.gz **-d** descriptions.txt \| bgzip **-c** \>out.vcf.gz

### Where descriptions.txt contains:

-

  key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'