Remove non-biallelic loci from a VCFArrow object
Details
This function removes non-biallelic loci from a VCFArrow object, returning a new VCFArrow object.
Examples
f <- system.file("extdata", "vaillantii_discosnp_sub.vcf.gz",
package = "VCFArrow")
vcf <- read_vcf(f) |> set_vcf_groups(dirname(f))
#> ℹ VCF is being read in chunks of 50000 variants
#> ✔ VCF successfully read into a VCFArrow object
vcf_filter_biallelic(vcf)
#> ℹ Applying biallelic filter
#> ℹ Retained 10000 / 10000 variants (biallelic SNVs)
#>
#> 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_1ff84e68e127
#>
#> 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