- Using the Haploview tool change vcf format file into the ped and info file .
example:
vcftools --gzvcf test.vcf.gz --plink --out HH
plink --file test --recode HV --out test
java -jar ~/biosoftware/Haploview.jar -n -pedfile example.ped -info example.info \
-maxdistance 1000 -minMAF 0.05 -hwcutoff 0 -dprime -memory 4096 -out test
- Then use the R script called from the command line to caculate the average LD values in each bin for the LD zone.
Rscript LD_decay_calculating_for_Haploview.R -i input.file -l 100000 -b 10000 -o output.file
- Using the vcftools to caculate the LD values .
example:
vcftools --vcf test.vcf --geno-r2 --ld-window-bp 100000 --out ld_window_100000 --min-r2 0.000001
awk '{if($1=="CHR"){print $0"\tDISTENCE"}else{print $0"\t"$3-$2}}' ld_window_100000.geno.ld > input.file
- Then use the R script called from the command line to caculate the average LD values in each bin for the LD zone.
Rscript LD_decay_calculating_for_vcftools.R -i input.file -l 100000 -b 10000 -o output.file
- The help manual is as follows：
Usage: LD_decay_calculating.R [options] args
Options:
-i CHARACTER, --input=CHARACTER
Input file name. The file output from Haploview. [required]
-l INTEGER, --LD_length=INTEGER
The farthest distance betweent two SNPs, Unit:bp. [required]
-b INTEGER, --bin_size=INTEGER
The bin size to caculating the avagerage LD, Unit:bp. [required]
-o CHARACTER, --output=CHARACTER
output file name [default= LD_decay_out.txt]
-h, --help
Show this help message and exit