DANNsweeps/data_process_documentation.txt at main · garudlab/DANNsweeps · GitHub

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# check num of individuals
plink --bfile v40.3.BA --freq --out tmp/freq_BA
grep "people" freq_BA.log # should give 177

#check average missing data per site
plink --bfile v51.0.H --missing --out tmp/missing_data_H
awk 'NR > 1 { total += $5; count++ } END { print total/count }' tmp/missing_data_H.lmiss

#convert to vcf
plink --bfile v51.0.H --recode vcf --out tmp/data_H.vcf

#extract chrom 2 from epoch H

plink --bfile v51.0.H --chr 2 --make-bed --out ../Chr2_H/v51.0.H.chr2

#convert to vcf in /u/project/ngarud/Garud_lab/aDNA/Chr2_H
plink --bfile v51.0.H.chr2 --recode vcf --out VCF.v51.0.H.chr2


## do this for all chromsomes

for chr in {1..22}; do
    #extract chrom
    plink --bfile ../DANN_DATA/v40.3.M --chr $chr --make-bed --out v40.3.M.chr$chr

    #convert to vcf
    plink --bfile v40.3.M.chr$chr --recode vcf --out VCF.v40.3.M.chr$chr

    rm v40.3.M.chr$chr*
    rm *log

done

for chr in {1..22}; do
    #extract chrom
    plink --bfile  DANN_DATA/YRI/v40.3.YRI --chr $chr --make-bed --out v40.3.YRI.chr$chr

    #convert to vcf
    plink --bfile v40.3.YRI.chr$chr --recode vcf --out YRI/VCF.v40.3.YRI.chr$chr

    rm -f v40.3.YRI.chr$chr*
    rm -f *log

done


#extract region that includes LCT
plink --bfile v51.0.H --chr 2 --from-bp 135408034 --to-bp 136308034 --make-bed --out ../Chr2_H/v51.0.H.chr2.LCT
#convert to vcf in /u/project/ngarud/Garud_lab/aDNA/Chr2_H
plink --bfile v51.0.H.chr2.LCT --recode vcf --out VCF.v51.0.H.chr2.LCT

# HLA region IA
plink --bfile v51.0.IA --chr 6 --from-bp 28138809 --to-bp 28910235 --make-bed --out ../Chr6_IA/v51.0.IA.chr6.HLA
#convert to vcf in /u/project/ngarud/Garud_lab/aDNA/Chr2_H
plink --bfile v51.0.IA.chr6.HLA --recode vcf --out VCF.v51.0.IA.chr6.HLA

#extract random region chrom2
plink --bfile v51.0.H --chr 2 --from-bp 203169 --to-bp 1103169 --make-bed --out ../Chr2_H/v51.0.H.chr2.region
#convert to vcf in /u/project/ngarud/Garud_lab/aDNA/Chr2_H
plink --bfile v51.0.H.chr2.region --recode vcf --out VCF.v51.0.H.chr2.region