Issue in computing the site frequency spectrum statistics using Rehh package
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2.1 years ago

Dear all,

I am using rehh package on R software to compute site frequency spectrum (sfs) statistics on a single chromosome of my pooled-seq data of 12 individuals. First, I converted my unphased vcf file to an object of class haplohh using the command

hp_vcf <- data2haplohh(hap_file = "sample.vcf", polarize_vcf = FALSE, vcf_reader = "vcfR", chr.name = "CM004588.1", verbose = TRUE)

Then, I used the function calc_sfs_tests. My command was

Sample <- calc_sfs_tests(hp_vcf, polarized = FALSE, window_size = 150000, overlap = 75000, right = TRUE, verbose = TRUE)

Below is the image of output generated.

Here is the image of the output

Now, I am stuck at this point. Kindly help me out that why there are zeros in last three columns and same values in theta's columns? where I am getting wrong? and what is the solution now? Any help would be highly appreciated.

Rehh R • 324 views
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