run_mapex: Run the mapex algorithm

In bmannakee/mapexr: Sensitive and Specific Filtering of Genetic Variants in Xenograft and Primary Tumors

Description

Run the mapex algorithm

Usage

run_mapex(bam_file, bam_idx, variant_file, variant_file_type = "maf",
  blast_out_file = NULL, blastn_path, blast_db_path, blast_threads = 1,
  min_mapq = 1)

Arguments

bam_file	Alignment file for the tumor sample to filter in bam format
bam_idx	Index for the alignment in bam_file
variant_file	variant call file in maflite, vcf, call_stats, or snp (varscan) format
variant_file_type	type of variant call file either maf (default maflite format), vcf (version >= 4.0), call_stats (MuTect1 format), or snp (Varscan2 format)
blast_out_file	file name for returned blast hits (default=NULL, do not output scored reads)
blastn_path	Path to a local installation of BLASTN
blast_db_path	Path to a BLAST database (typically human/mouse reference or human reference)
blast_threads	Number to threads to run blast with (default=1)
min_mapq	Minimum read mapping quality score (default=1)

Value

a data frame with four columns; chrom the chromosome the variant is on,loc the position of the variant variant_score the variant score between 0 and 1, and reason the variant classification which takes values mouse, off_target, or on_target.

Examples

## Not run: 
## file paths and variables
bam <- "/path/to/tumor.bam"
bamidx <- "/path/to/tumor.bai"
variants <- "/path/to/variants.vcf"
blastout <- "/path/to/blastoutput.txt" # Read level blast results, not required
blastpath <- "/path/to/blastn" # if blast is in the users path, just "blastn" here
blastdb <- "/path/to/combined_db"
threads <- 1 # number of threads consumed by blastn
mapq <- 1 # this is the default for minimum mapq score
results <- run_mapex(bam_file=bam,
                     bam_idx=bamidx,
                     variant_file=variants,
                     variant_file_type='vcf',
                     blast_out_file=blastout,
                     blastn_path=blastpath,
                     blast_threads=threads,
                     min_mapq=mapq)

## End(Not run)

bmannakee/mapexr documentation built on May 5, 2019, 12:27 p.m.