-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpca.sh
23 lines (20 loc) · 1.24 KB
/
pca.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
#!/bin/sh
filename=84-81.1_18.SNP.filtered.PASS.novariants.cluster.windows.wms.vcf.gz
WD=/projects/whj-chenhm/pig/labdata/05vcfnew/
WD6=/projects/whj-chenhm/pig/labdata/06vcf_pca/
gcta64=/projects/whj-chenhm/bin/gcta_1.94.0beta/gcta64
$gcta64 --thread-num 40 --make-grm --out ${WD6}${filename}.gcta --bfile ${WD}${filename} --autosome-num 18
$gcta64 --thread-num 40 --grm ${WD6}${filename}.gcta --pca 20 --out ${WD6}${filename}.gcta &
plink --chr-set 18 --noweb --bfile ${WD}${filename} --pca 20 --genome --out ${WD6}${filename}
perl vcf_pca_tree.pl
###
filename=DNBN.1_18.SNP.filtered.PASS.novariants.cluster.windows.wms.vcf.gz
WD=/projects/whj-chenhm/pig/labdata/06vcf_diannan_banna/
WD6=/projects/whj-chenhm/pig/labdata/06vcf_pca/
gcta64=/projects/whj-chenhm/bin/gcta_1.94.0beta/gcta64
vcftools --gzvcf ${WD}${filename} --plink --out ${WD}${filename}
plink --noweb --file ${WD}${filename} --make-bed --out ${WD}${filename}
$gcta64 --thread-num 40 --make-grm --out ${WD6}${filename}.gcta --bfile ${WD}${filename} --autosome-num 18
$gcta64 --thread-num 40 --grm ${WD6}${filename}.gcta --pca 20 --out ${WD6}${filename}.gcta &
plink --chr-set 18 --noweb --bfile ${WD}${filename} --pca 20 --genome --out ${WD6}${filename}
perl vcf_pca_tree.pl