Gets reads fragment lengths for a list of mutations

The function extracts the fragment lengths for the reads holding alternative allele for each mutation in the mutations data frame.

get_mutations_fragment_size(bam, mutations, tag = "",
  min_base_quality = 20, min_mapq = 30, ...)

Arguments

bam	path to bam file.
mutations	Data frame with mutations. Must have the columns CHROM, POS, REF, ALT.
tag	the RG tag if the bam has more than one sample.
min_base_quality	minimum base quality when extracting reads covering mutations.
min_mapq	minimum mapping quality when extracting reads covering mutations.
...	Other parameters passed to get_fragment_size.

Value

A list with length equal to the number of mutations. Each element contains a list with two elements ref and alt each having an integer vector of fragment lengths

Details

Fragment length will extracted from the bam file according to the parameters passed to get_fragment_size, and the fragment size of the reads that map to the ref and alt alleles of each mutation in the input will be returned.

See also

get_fragment_size

Examples

# \donttest{
data("mutations", package = "ctDNAtools")
bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")

mfs <- get_mutations_fragment_size(bam = bamT1, mutations = mutations[1:2, ])
# }