Identify SNVs, Insertions and Deletions within a GRanges object
varTypes(x, alt_col = "ALT", ...)GenomicRanges object
Name of the column with mcols(x) which contains the alternate allele. Can be an XStringSetList, XStringSet or character
Not used
Character vector
Using the width of the reference and alternate alleles, classify each range as an SNV, Insertion or Deletion.
SNVs are expected to have REF & ALT widths of 1
Insertions are expected to have ALT longer than REF
Deletions are expected to have ALT shorter than REF
These are relatively permissive criteria
# Load the example VCF and classify ranges
library(VariantAnnotation)
f <- system.file("extdata/1000GP_subset.vcf.gz", package = "transmogR")
vcf <- readVcf(f)
gr <- rowRanges(vcf)
type <- varTypes(gr)
table(type)
#> type
#> Deletion Insertion SNV
#> 6 1 93
gr[type != "SNV"]
#> GRanges object with 7 ranges and 5 metadata columns:
#> seqnames ranges strand | paramRangeID
#> <Rle> <IRanges> <Rle> | <factor>
#> 1:788418:CAG:C chr1 788418-788420 * | NA
#> 1:789568:TATGGA:T chr1 789568-789573 * | NA
#> 1:790933:CGAATGGAAT:C chr1 790933-790943 * | NA
#> 1:818464:CCT:C chr1 818464-818466 * | NA
#> 1:826577:A:AT chr1 826577 * | NA
#> 1:839480:CACACACCTG:C chr1 839480-839494 * | NA
#> 1:839515:CTAGACACAC:C chr1 839515-839543 * | NA
#> REF ALT QUAL
#> <DNAStringSet> <DNAStringSetList> <numeric>
#> 1:788418:CAG:C CAG C NA
#> 1:789568:TATGGA:T TATGGA T NA
#> 1:790933:CGAATGGAAT:C CGAATGGAATG C NA
#> 1:818464:CCT:C CCT C NA
#> 1:826577:A:AT A AT NA
#> 1:839480:CACACACCTG:C CACACACCTGGACAA C NA
#> 1:839515:CTAGACACAC:C CTAGACACAC...CACACACACG C NA
#> FILTER
#> <character>
#> 1:788418:CAG:C .
#> 1:789568:TATGGA:T .
#> 1:790933:CGAATGGAAT:C .
#> 1:818464:CCT:C .
#> 1:826577:A:AT .
#> 1:839480:CACACACCTG:C .
#> 1:839515:CTAGACACAC:C .
#> -------
#> seqinfo: 1 sequence from an unspecified genome