Compute FST and visualize in manhattan plot with qqman r package

This tutorial shows you how to compute FST values and visualize in a manhattan plot
Course material
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Install VCFTOOLS
binaries: • How to Install VCFTOOL...
anaconda: • Video
How to install R
Linux(Ubuntu): • Install, Configure and...
Using anaconda: • Install, Configure and...
Original data source
www.malariagen...
Download the vcf here:
github.com/vap...
Download the R script here
github.com/vap...
qqman documentation
rdrr.io/cran/q...
cran.r-project...
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Sections of this video
00:04 intro
00:44 pc requirement
01:13 download the example data
04:13 get the sample ids for the population of interests
09:15 compute fst values
11:12 inspect the output files
13:30 download the R script for generating the manhattan plot
14:56 open the R script using R studio
16:41 load the qqman R package
16:44 set the working directory
17:38 read load the fst values
18:45 add snp information
21:04 generate manhattan plots
22:46 change the color of the manhattan plots
24:01 annotate snps that have particular fst values
27:17 draw a genomewide line on the manhattan plot
30:42 highlight snps of interest
Music
Buddha by Kontekst / kontekstmusic
Creative Commons - Attribution-ShareAlike 3.0 Unported - CC BY-SA 3.0
Free Download / Stream: bit.ly/2Pe7mBN
Music promoted by Audio Library • Buddha - Kontekst (No ...
#bioinformatics #bioinformática #bioinformaticsforbeginners
#rprogrammingforbeginners #rtutorial
population genetics
commands used in this tutorial
vcftools query
vcftools --weir-fst-pop

[@BilalAhmad-y8r4f]

My fst values are -nan and values less than 0. Can we replace -nan with 0.

[@danieladediran3228]

Well explanatory, thanks for this and looking forward to more tutorials on gwas

[@aqilfarooq3808]

canu help i have vcf fil and i want to compute fst