get_mutations_read_names: Gets names of the reads showing reference and alternative...
In alkodsi/ctDNAtools: Analyze Circulating Tumor DNA Sequencing Data

Description Usage Arguments Details Value See Also Examples

View source: R/get_mutations_read_names.R

This function extracts the names of the reads in a bam file that support the variant and reference alleles of the input mutations

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

`bam`	path to bam file
`mutations`	A data frame containing the mutations. Must have the columns CHROM, POS, REF, ALT.
`min_base_quality`	integer specifying the minimum base quality for reads to be included.
`tag`	the RG tag if the bam has more than one sample
`min_mapq`	integer specifying the minimum mapping quality for reads to be included

Returns the IDs of the read that cover the input mutations (ref and alt alleles).

A list with length equal to the number of mutations. Each element is a character vector with the read names.

get_mutations_read_counts get_mutations_fragment_size test_ctDNA

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data("mutations", package = "ctDNAtools")
bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
get_mutations_read_names(bam = bamT1, mutations = mutations[1:3, ])