## ----message = FALSE---------------------------------------------------------- library(SICtools) ## ----------------------------------------------------------------------------- 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') snpDiffDf <- snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,baseDistCutOff=0) snpDiffDf ## ----------------------------------------------------------------------------- snpDiffDfSort <- snpDiffDf[order(snpDiffDf$p.value,snpDiffDf$d.value),] snpDiffDfSort ## ----------------------------------------------------------------------------- indelDiffDf <- indelDiff(bam1,bam2,refFsa,'chr07',828514,828914,pValueCutOff=1,gtDistCutOff=0) indelDiffDfSort <- indelDiffDf[order(indelDiffDf$p.value,indelDiffDf$d.value),] indelDiffDfSort ## ----------------------------------------------------------------------------- sessionInfo()