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Old 04-08-2015, 03:01 AM   #1
man4ish
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Location: OK

Join Date: Jan 2010
Posts: 7
Default How to calculate LD in 2 direction?

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?

Last edited by man4ish; 04-08-2015 at 05:05 AM.
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