seqAsVCF {SeqArray} | R Documentation

## VariantAnnotation objects

### Description

Create a VCF-class object

### Usage

    seqAsVCF(x, chr.prefix="", info=NULL, geno=NULL)

### Arguments

`x` | a `SeqVarGDSClass` object
`chr.prefix` | prefix to add to seqlevels
`info` | which INFO fields to return
`geno` | which GENO fields to return

### Details

Coerces a SeqVarGDSClass object to a VCF-class object. Row names correspond to the variant.id. `info` and `geno` specify the 'INFO' and 'GENO' (FORMAT) fields to return, respectively. If not specified, all fields are returned; if 'NA' no fields are returned. Use `seqSetFilter` prior to calling `seqAsVCF` to specify samples and variants to return.

The VariantAnnotation package should be loaded to explore this object.

### Value

A `CollapsedVCF` object.

### Author(s)

Stephanie Gogarten, Xiuwen Zheng

### See Also

`VCF-class`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))

    ## Not run:
    library(VariantAnnotation)
    seqAsVCF(gds)

    ## End(Not run)

    seqClose(gds)

[Package SeqArray version 1.26.2 Index]