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Identify SNVs, Insertions and Deletions

Source: R/varTypes.R
varTypes.Rd

Identify SNVs, Insertions and Deletions within a GRanges object

Usage

varTypes(x, alt_col = "ALT", ...)

Arguments

x

GenomicRanges object

alt_col

Name of the column with mcols(x) which contains the alternate allele. Can be an XStringSetList, XStringSet or character

...

Not used

Value

Character vector

Details

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

Examples

# 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