SR4R SnpReady for Rice

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Population diversity analysis

Description:

Build a phylogenetic tree (NJ tree) for and provided ped format file.

Usage:

perl plink2fasta.pl test21.ped > test21.output.fa MEGA7/megacc -a MEGA7/template.mao -d test21.output.fa

Input file:

test21.ped, template.mao

Output files:

M7CC_Out/test21.output-*.nwk

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Description:

Perform a PCA analysis for provided ped+map files.

Usage:

plink --file test22 --make-bed flashpca --bfile plink

Input file:

test22.ped, test22.map

Output files:

pcs.txt, pve.txt

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Description:

To perform a structure analysis for provided ped+map files

Usage:

plink --file test23 --make-bed python fastStructure-master/structure.py -K 3 --input plink --output K

Input file:

test23.ped, test23.map

Output files:

K.3.meanQ

Parameters:

k=[2/3/4/5/6/7/8]

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Description:

Calculate pairwise IBS values for provided ped+map files.

Usage:

plink --file test24 --distance ibs flat-missing square

Input file:

test24.ped, test24.map

Output files:

plink.mibs

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Description:

Detect ROH for a provided ped+map files.

Usage:

plink --file test25 --homozyg --homozyg-kb 200 --homozyg-snp 1000 --homozyg-het 0.001

Input file:

test25.ped, test25.map

Output files:

plink.hom

Parameters:

--homozyg-kb=200, --homozyg-snp=1000, --homozyg-het=0.001

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Description:

Calculate LD values for pairwise SNPs for provided ped+map file.

Usage:

plink --file test26 --r2 --ld-window 10000 --ld-window-kb 1000 --ld-window-r2 0 --maf 0.05

Input file:

test26.ped, test26.map

Output files:

plink.ld

Parameters:

--ld-window=10000, --ld-window-kb=1000, --ld-window-r2=0, --maf=0.05

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Description:

Calculate sites or windowed pi values for a provided vcf file.

Usage:

#site
vcftools --vcf test27.vcf --out test27.output --site-pi #window
vcftools --vcf test27.vcf --out test27.output --window-pi 1000

Input file:

test27.vcf

Output files:

test27.output.sites.pi OR test27.output.windowed.pi

Parameters:

--window-pi=[window size] (for window mode)

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Description:

Calculate windowed tajima’D values for a provided vcf file.

Usage:

vcftools --vcf test28.vcf --out test28.output --TajimaD 1000

Input file:

test28.vcf

Output files:

test28.output.Tajima.D

Parameters:

--TajimaD=[window size]

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Description:

Calculate sites or windowed fst values for provided vcf file and two list files.

Usage:

#site
vcftools --vcf test29.vcf --out test29.output --weir-fst-pop test29.lista --weir-fst-pop test29.listb #window
vcftools --vcf test29.vcf --out test29.output --weir-fst-pop test29.lista --weir-fst-pop test29.listb --fst-window-size 1000

Input file:

test29.vcf

Output files:

test29.output.weir.fst OR test29.output.windowed.weir.fst

Parameters:

--weir-fst-pop=[list1], --weir-fst-pop=[list2], --window-pi=[window size] (for window mode)

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