Plotting Snps Over Contigs-Sliding Window

Question

[jackuser1979]

I have VCF file format with SNPs predicted. I would like to plot these SNPs/contig wise through sliding window. Is there any script or R package available already?

Answer 1

[Zev.Kronenberg]

You can use the ZOO package in [R]. I also have an R script to do it (It is C under the hood).

Here is the github link:

https://github.com/jewmanchue/ZevRTricks

genomicwindowmean.R <- the [r] script

mean_window.c <- the accompanying C program

For your purpose you would need to edit line 29 to make it a count rather than an average.

[jackuser1979]

Thanks. I will look into ZOO package. If possible can you share your script?