catchMismatch: Catch mismatch positions from BAM files

In TapscottLab/SeqPipelineTools: Pipeline tools for RNA-seq or ChIP-seq data

Usage

catchMismatch(bam_file, BSgenome, snps = NULL,
    BSgenomeInjectSNP = NULL,
    include_deletions = FALSE, include_insertions = FALSE,
    min_base_quality = 10, min_nucleotide_depth = 1,
    min_mapq = 10, max.mismatch = 10)

Arguments

bam_file	A character string specifying the bam file.
BSgenome	BSGenome object of the reference genome.
snps	A GRange object of SNP position on the reference genome.
BSgenomeInjectSNP	BSgenome object injected with SNP. See details.
include_deletions	A logical specifying whether the pileup should include deletion.
include_insertions	A logical specifying whether the pileup should include insertions.
min_base_quality	A locial indicating the minimum base quality score.
min_nucleotide_depth	An integer indicating the mininum depth of nucleotide.
min_mapq	An integer indicating the mininum MAPQ score.
max.mismatch	an integer indicating the max. mismatch of a read.

Details

This function generates a data.frame of mismatch nucleotides and the type of mismatch relative to the reference genome. See example.

Value

A data.frame includes columns of mismatch position, nucleotides, nucleotides depth, reference nucleotides and mismatch type.

Author(s)

Chao-Jen Wong <[e-mail]>

See Also

tallyWrapper

Examples

## Not run: 
mainDir <- "/fh/fast/tapscott_s/CompBio/RNA-Seq/hg38.dsRNA"
bamDir <- "/fh/fast/tapscott_s/CompBio/RNA-Seq/Sean/MB135_dsRNA/hg38_bwa"
bam_file <- file.path(bamDir, "Sample_mb135_wDox_k1.sorted.bam")

library(BSgenome.Hsapiens.UCSC.hg38)
library(parallel)
library(rtracklayer)
library(Rsamtools)
snps <- get(load(file="/fh/fast/tapscott_s/CompBio/hg38/FDb.UCSC.snp147Common.hg38/data/snp147common.GR.rda"))
BSgenome <- BSgenome.Hsapiens.UCSC.hg38
tally <- catchMismatch(bam_file=bam_file, BSgenome=BSgenome, snps=snps,
                       min_base_quality=10,
                       min_nucleotide_depth=2,
                       include_deletions=FALSE,
                       include_insertions=FALSE,
                       min_mapq=10, max.mismatch=10)
SeqPipelineTools:::freqAIMismatch(tally, exclude.SNP=FALSE)

## End(Not run)

TapscottLab/SeqPipelineTools documentation built on May 16, 2019, 2:28 a.m.