read_vcf — read_vcf • VCFArrow

Read VCF file and store its content within a VCFArrow object

Usage

read_vcf(vcf_file, chunk_size = 50000)

Arguments

vcf_file: -> VCF file
chunk_size: -> number of variants to read in at a time, default 50000 (integer)

Value

VCFArrow object

Details

This function read a VCF file into an S4 class object in chunks, returning a VCFArrow object. It accepts both uncompressed and gz compressed files. The GT field is stored as an Apache Arrow in Long format. Various metrics are precalculated for fast and easy filtering. GT slot content stored in a TEMP directory for lazy loading.

Author

Tomas Hrbek April 2026

Examples

f <- system.file("extdata", "vaillantii_discosnp_sub.vcf.gz",
                 package = "VCFArrow")
vcf <- read_vcf(f)
#> ℹ VCF is being read in chunks of 50000 variants
#> ✔ VCF successfully read into a VCFArrow object
vcf
#> 
#> An object of class "VCFArrow"
#> 
#> Dimensions:
#>   Variants: 10000 
#>   Samples:  18 
#> 
#> Quick stats:
#>   Non-missing variants: 10000 
#> 
#> Phased genotypes: FALSE 
#> 
#> Storage:
#>   Path: /tmp/RtmpSpcr9J/arrow_vcf_1ff872600358 
#> 
#> Genotype storage (Arrow):
#> FileSystemDataset with 1 Feather file
#> 9 columns
#> .row_id: int32
#> sample: string
#> a1: int32
#> a2: int32
#> phased: bool
#> fmt: string
#> DP: double
#> GQ: double
#> ADR: double
#> 
#> See $metadata for additional Schema metadata
#> 
#> Variants (first 5 rows):
#>                     CHROM POS        ID REF ALT QUAL FILTER Rk RPT n_alt
#> 1 SNP_higher_path_9994239  41 9994239_1   C   G    .      .  1  NA     1
#> 2 SNP_higher_path_9984432 105   9984432   C   T    .      .  1  NA     1
#> 3 SNP_higher_path_9967574  50   9967574   A   C    .      .  1  NA     1
#> 4  SNP_higher_path_993510  88  993510_4   A   G    .      .  1  NA     1
#> 5 SNP_higher_path_9803974  33   9803974   A   G    .      .  1  NA     1
#>   is_biallelic is_indel .row_id
#> 1         TRUE    FALSE       1
#> 2         TRUE    FALSE       2
#> 3         TRUE    FALSE       3
#> 4         TRUE    FALSE       4
#> 5         TRUE    FALSE       5
#>   ... 9995 more
#> 
#> INFO (first 5):
#> [1] "Ty=SNP;Rk=1.0;UL=11;UR=8;CL=11;CR=27;Genome=.;Sd=.;Cluster=20022615;ClSize=3"
#> [2] "Ty=SNP;Rk=1.0;UL=3;UR=1;CL=75;CR=7;Genome=.;Sd=.;Cluster=17296599;ClSize=1"  
#> [3] "Ty=SNP;Rk=1.0;UL=20;UR=4;CL=20;CR=4;Genome=.;Sd=.;Cluster=18266172;ClSize=3" 
#> [4] "Ty=SNP;Rk=1.0;UL=1;UR=0;CL=1;CR=0;Genome=.;Sd=.;Cluster=16400006;ClSize=2"   
#> [5] "Ty=SNP;Rk=1.0;UL=3;UR=7;CL=3;CR=7;Genome=.;Sd=.;Cluster=10880986;ClSize=5"   
#> 
#> FORMAT (first 5):
#>           FORMAT .row_id
#> 1 GT:DP:PL:AD:HQ       1
#> 2 GT:DP:PL:AD:HQ       2
#> 3 GT:DP:PL:AD:HQ       3
#> 4 GT:DP:PL:AD:HQ       4
#> 5 GT:DP:PL:AD:HQ       5
#> 
#> Samples (first 5):
#> [1] "Pv120" "Pv126" "Pv13"  "Pv14"  "Pv27" 
#>   ... 13 more