How to Extract Values for SNPs by each chromosome and position using --window

Question

[Raju]

Hello Folks, How to extract values or data for SNPs rs11020655 & rs7277175 by each chromosome using .bed file I have tried this

%%bash
# --from-kb 0 --to-kb 1000
for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y M
do
       plink --bfile Obesity_Send --chr %i --recode --out chr-%i-results --noweb
done

please help

[Pierre Lindenbaum]

if you do have a bed file overlapping the two snps and your vcfs are indexed, the command should be:

bcftools concat -a --file-list file_containing_the_path_to_the_vcfs.txt --regions-file input.bed