get_mutations_read_counts: Counts ref and alt reads for a set of mutations
In ctDNAtools: Analyze Circulating Tumor DNA Sequencing Data

Description Usage Arguments Details Value See Also Examples

View source: R/get_mutations_read_counts.R

Counts ref and alt reads for a set of mutations in a bam file

1 2	get_mutations_read_counts(mutations, bam, tag = "", min_base_quality = 20, max_depth = 1e+05, min_mapq = 30)

`mutations`	A data frame with the reporter mutations. Should have the columns CHROM, POS, REF, ALT.
`bam`	path to bam file
`tag`	the RG tag if the bam has more than one sample
`min_base_quality`	minimum base quality for a read to be counted
`max_depth`	maximum depth above which sampling will happen
`min_mapq`	the minimum mapping quality for a read to be counted

Quantifies the reference and variant alleles for the input mutations in the input bam file. Useful for forced calling mutations.

a named list contains: ref, vector of read counts of the reference alleles, and alt, vector of read counts of the alternative allele

get_mutations_read_names test_ctDNA get_mutations_fragment_size

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