SNP density

Question

[Shin Taguchi]

Hi, everyone.

I would like to create a figure plotting SNP density for each chromosome from a vcf file. All I have on hand now is the vcf file after the SNP call. If anyone knows of any software suitable for this, please tell me.

Otherwise, any help or advice would be much appreciated. It must be doable because I see plenty of published papers with SNP density plotted against chromosome position, but I can't figure out how to do it myself.

Thank you very mach.

Taguchi

[Pierre Lindenbaum]

snp density plot ; Plotting Density Of Snps On Chromosomes ; Plotting SNP density heatmap chromosome ideogram ; Plotting SNP density along a chromosome from VCF files ; ...

[Shin Taguchi]

Hi, Pierre

I thought this post is nearest to my situation and need. snp density plot

And I have another question about the script in this post. What does it mean "data.txt" in this script ? Is it name of input vcf file ?

library(karyoploteR)

#Read the data
vars <- read.table("data.txt", comment.char = "", header = TRUE)

#Build a GRanges and convert chromosome names from "1" to "chr1" 
vars <- toGRanges(vars[,c(1,2,2,3:length(vars))])
seqlevelsStyle(vars) <- "UCSC"

#Plot SNPs as Points
kp <- plotKaryotype(genome="hg19")
kpPoints(kp, data=vars, y=0.5)

#Plot SNPs as density
kp <- plotKaryotype(genome="hg19")
kpPlotDensity(kp, data=vars)

[Shin Taguchi]

@Pierre Lindenbaum Thank you for your advice !