subset_bam: Subset a bam for specific chromome(s) or ranges based on...

In jennylsmith/fusBreakpoint: Find fusion exon junction sequence reads from RNAseq BAM files

Description

Subset a bam for specific chromome(s) or ranges based on input breakpoint or fusion data file.

Usage

subset_bam(
  Sample_ID,
  breakpoint = NULL,
  fusion_data = NULL,
  file_manifest,
  by_chr = FALSE,
  scan = FALSE,
  Seqlens = NULL,
  outdir = file.path("/fh/scratch/delete90/jlsmith3/subset_bams")
)

Arguments

Sample_ID	character string of patient ID
breakpoint	character vector with breakpoint string (can be named)
fusion_data	dataframe with fusion results from CICERO, TransAbyss, and STAR-Fusion concatenated
file_manifest	dataframe with Sample_ID and the full file path of the BAM file.
by_chr	boolean - get reads mapped to the entire chromosome containing the breakpoint or just +/- 1e6 bp from breakpoint
scan	boolean - read into memory or not
Seqlens	named numeric vector with chromosome lengths
outdir	destination for subsetted bam files if scan = FALSE

Examples

## Not run: 
my_files_df <- data.frame(Sample="PAZZUM.03A.01R", filepath=dir("/path/to/sample.bam"))
subset_bam("PAZZUM.03A.01R", breakpoint=list("16:1250000|16:1260000"), my_files_df)

## End(Not run)

jennylsmith/fusBreakpoint documentation built on Oct. 7, 2021, 8:04 p.m.