snpDiff: main function to test point differences between the two bam...

In SICtools: Find SNV/Indel differences between two bam files with near relationship

Description

test base count (A,T,G,C) difference at a given position between the two bam files. The base count matrix is tested by fisher exact test and euclidean distance. If nothing difference, NULL will be returned.

Usage

snpDiff(bam1, bam2, refFsa, regChr, regStart, regEnd, minBaseQuality = 13, minMapQuality = 0, nCores = 1, pValueCutOff = 0.05, baseDistCutOff = 0.1,verbose = TRUE)

Arguments

bam1	the first bam file to be compared
bam2	the second bam file to be compared
refFsa	the reference fasta file used for bam1 and bam2 alignments
regChr	chromosome name of the region of interest, it should match the chromosome name in reference name
regStart	the start position (1-based) of the region of interest
regEnd	the end position (1-based) of the region of interest
minBaseQuality	the minimum base quality to be used for base count
minMapQuality	the minimum read mapping quality to be used for base count
nCores	number of thread used for calculate in parallel
pValueCutOff	p.value cutoff from fisher.test to display output. If there is no difference between two compared positions (p.value = 1 and d.value = 0), NULL will be returned even setting pValueCutOff = 1.
baseDistCutOff	euclidean distance cutoff from dist(,method='euclidean') to display output. If there is no difference between two compared positions (p.value = 1 and d.value = 0), NULL will be returned even setting baseDistCutOff = 0.
verbose	print progress on screen, default = TRUE.

Value

snpDiff: returns a data.frame with difference information: chromosome, position, reference base, base count (A,C,G,T,N) for two bam files, p.value (fisher exact test of these base counts) and d.value (euclidean distance of these base counts)

Author(s)

Xiaobin Xing, <email:[e-mail]>

References

Morgan M, Pages H, Obenchain V and Hayden N. Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import.

Examples

bam1 <- system.file(package='SICtools','extdata','example1.bam')
bam2 <- system.file(package='SICtools','extdata','example2.bam')
refFsa <- system.file(package='SICtools','extdata','example.ref.fasta')

snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,baseDistCutOff=0)

SICtools documentation built on Nov. 8, 2020, 5:12 p.m.