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LD-decay-calculating

Directions

The first Method for Haploview outputs

  • 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

The second Method for vcftools outputs

  • 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