Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • man4ish
    started a topic How to calculate LD in 2 direction?

    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, 05:05 AM.

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 04:11 PM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
34 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
56 views
0 likes
Last Post seqadmin  
Working...
X