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Plotting Snps Over Contigs-Sliding Window

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?

r
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updated by Ram Ram • written by jackuser1979 jackuser1979

1 answer

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.

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written by Zev.Kronenberg Zev.Kronenberg

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

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written by jackuser1979 jackuser1979

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