Hi,
I have list of snps in vcf format and i need to calculate LD in such a way that window should be +_90 either side.
I tried both plink and vcf-tools but both works in forward direction(i.e 3rd column value is greater than 2nd column value).
vcftools --vcf testset --hap-r2 --ld-window-bp 10000 --out OUTFILE
Sample Output
CHR POS1 POS2 N_CHR R^2 D Dprime
11 60250005 60250039 1008 1.19644e-05 -1.18103e-05 -1
11 60250005 60250058 1008 6.84498e-05 -6.39723e-05 -1
11 60250039 60250058 1008 0.000830469 -0.000767668 -1
11 60250039 60250096 1008 -nan 0 -nan
11 60250039 60250125 1008 -nan 0 -nan
11 60250058 60250096 1008 -nan 0 -nan
11 60250058 60250125 1008 -nan 0 -nan
11 60250058 60250140 1008 -nan 0 -nan
11 60250096 60250125 1008 -nan 0 -nan
11 60250096 60250140 1008 -nan 0 -nan
11 60250096 60250157 1008 -nan 0 -nan
11 60250125 60250140 1008 -nan 0 -nan
11 60250125 60250157 1008 -nan 0 -nan
11 60250140 60250157 1008 -nan 0 -nan
11 60250140 60250230 1008 -nan 0 -nan
11 60250157 60250230 1008 -nan 0 -nan
11 60250230 60250267 1008 9.84931e-05 -9.64506e-05 -1
11 60250230 60250275 1008 0.0004662 -0.000434028 -1
11 60250267 60250275 1008 0.000938967 -0.000868056 -1
How can i get desired output?
I have list of snps in vcf format and i need to calculate LD in such a way that window should be +_90 either side.
I tried both plink and vcf-tools but both works in forward direction(i.e 3rd column value is greater than 2nd column value).
vcftools --vcf testset --hap-r2 --ld-window-bp 10000 --out OUTFILE
Sample Output
CHR POS1 POS2 N_CHR R^2 D Dprime
11 60250005 60250039 1008 1.19644e-05 -1.18103e-05 -1
11 60250005 60250058 1008 6.84498e-05 -6.39723e-05 -1
11 60250039 60250058 1008 0.000830469 -0.000767668 -1
11 60250039 60250096 1008 -nan 0 -nan
11 60250039 60250125 1008 -nan 0 -nan
11 60250058 60250096 1008 -nan 0 -nan
11 60250058 60250125 1008 -nan 0 -nan
11 60250058 60250140 1008 -nan 0 -nan
11 60250096 60250125 1008 -nan 0 -nan
11 60250096 60250140 1008 -nan 0 -nan
11 60250096 60250157 1008 -nan 0 -nan
11 60250125 60250140 1008 -nan 0 -nan
11 60250125 60250157 1008 -nan 0 -nan
11 60250140 60250157 1008 -nan 0 -nan
11 60250140 60250230 1008 -nan 0 -nan
11 60250157 60250230 1008 -nan 0 -nan
11 60250230 60250267 1008 9.84931e-05 -9.64506e-05 -1
11 60250230 60250275 1008 0.0004662 -0.000434028 -1
11 60250267 60250275 1008 0.000938967 -0.000868056 -1
How can i get desired output?
