GetAllBAMSlicesSamtools: Get and save all slices of BAM as specified by positions in a...

In steverozen/DBSverify: Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

Description

Get and save all slices of BAM as specified by positions in a VCF table.

Usage

GetAllBAMSlicesSamtools(
  vcf,
  bam.name,
  padding = 10,
  where.to.put.slices = tempfile(),
  verbose = 0
)

Arguments

vcf	A VCF (Variant Call Format) "file" as a data.table or similar.
bam.name	The file name (path) to the BAM file to slice.
padding	How many base pairs on each side of the first base of the DBS to to keep in the BAM slices.
where.to.put.slices	If NULL, create a temporary directory to store the slices. Otherwise, a character string that specifies a directory in which to store the BAM slices. This is directory is created if necessary.
verbose	If > 0 print a message when starting the number of slices generated every verbose slices.

Value

A character string that specifies the directory the containing the BAM slices. The slices are stored as SAM files.

steverozen/DBSverify documentation built on Dec. 23, 2021, 5:34 a.m.