bsaR

A simple R packages for bulk segregation analysis.

Installation

install.packages("vcfR")
remotes::install_github("xuzhougeng/bsaR")

Usage

The input file should be processed by the GATK, e.g "gatk-hc.final.snp.vcf.gz"

Step1: Create the BSA project from the vcf file

library(vcfR)
library(bsaR)

# Calculate the allele frequency ------------------------------------------
vcf.file <- "gatk-hc.final.snp.vcf.gz"

bsa <- CreateBsaFromVcf(vcf.file = vcf.file)

Step2: Filter the BSA with the following standard

• only keep bi
• exclude the NA row
• filter the only depth loci

bsa <- FilterMultiVariant(bsa)
bsa <- FilterNaVariant(bsa)

bsa <- CalcDepth(bsa)
bsa <- FilterLowDepth(bsa, depth = 40)

Step3: calculte the frequency

bsa <- CalcAltFreq(bsa)

Step3.5: filter the potential error loci with low frequency

Step4: Visualization

"sample1" and "sample2" should be sample name in the VCF file

# Visualization -----------------------------------------------------------

bsa <- CalcFreqByWindow(bsa, window.size = 5000)
# plot per contig
# plot for contig  ------------------------------------------------------

pdf("dotplot.pdf")
for (i in paste0("chr", 1:8)){
  plotWindowFreq(bsa, i, "sample1", "sample2",
                 window.size = 5000)
}
dev.off()