-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathroh.sh
36 lines (28 loc) · 1.63 KB
/
roh.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
WD6=/projects/whj-chenhm/pig/labdata/05vcfnew
WD65=$WD6/bethshapiro
mkdir ${WD65}
#/project-whj/chm/pig/labdata/yaqi_vcf/final_rawVariant.vcf.gz
cd $WD6
geno=84.1_18.SNP.filtered.PASS.vcf.gz
geno2=84.1_18.SNP.filtered.PASS.novariants.vcf.gz
geno3=84-81.1_18.SNP.filtered.PASS.novariants.cluster.windows.wms.vcf.gz
for K in $geno $geno2
do
{
# vcftools --gzvcf ${K} --plink --out ${WD6}/${K}
# plink --noweb --file ${WD6}/${K} --make-bed --out ${WD6}/${K}
# plink --bfile ${WD6}/${K} --homozyg --homozyg-kb 50 --homozyg-window-snp 50 --homozyg-snp 20 --homozyg-gap 1000 --allow-extra-chr --out ${WD66}/yaqi.${K}
# plink --file ${WD6}/${K} --homozyg --homozyg-window-snp 20 --homozyg-kb 10 -allow-no-sex --noweb --homozyg-window-het 1 --homozyg-window-missing 20 --out ${WD67}/wgs.${K}
plink --file ${WD6}/${K} --homozyg-window-het 20 --homozyg-window-missing 20 --homozyg-window-threshold 0.02 --homozyg-het 750 --homozyg-kb 500 --out ${WD65}/bethshapiro.${K}
}> ${WD6}/${K}.log &
done
for K in $geno3
do
{
vcftools --gzvcf ${K} --plink --out ${WD6}/${K}
plink --noweb --file ${WD6}/${K} --make-bed --out ${WD6}/${K}
# plink --bfile ${WD6}/${K} --homozyg --homozyg-kb 50 --homozyg-window-snp 50 --homozyg-snp 20 --homozyg-gap 1000 --allow-extra-chr --out ${WD66}/yaqi.${K}
# plink --file ${WD6}/${K} --homozyg --homozyg-window-snp 20 --homozyg-kb 10 -allow-no-sex --noweb --homozyg-window-het 1 --homozyg-window-missing 20 --out ${WD67}/wgs.${K}
plink --file ${WD6}/${K} --homozyg-window-het 20 --homozyg-window-missing 20 --homozyg-window-threshold 0.02 --homozyg-het 750 --homozyg-kb 500 --out ${WD65}/bethshapiro.${K}
}> ${WD6}/${K}.log &
done