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hardingnj / xpclr

Code to compute the XP-CLR statistic to infer natural selection
MIT License
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Input files requirement for XP-CLR #89

Open dhimanamar opened 1 year ago

dhimanamar commented 1 year ago

Hi, I am working on whole-genome resequencing dataset of different cultivated (sugar, fodder, leaf and table) and wild beets. I would like to run selective sweep analysis using xpclr. I have already called and filtered my variants and based on the crop types, I have created different vcf files from each crop type. I have some questions regarding the input files for xp-clr, the questions are as follows:

  1. Do I need separate vcf files for each sub-population or simply I could use a vcf file from the whole panel and just use --samples flag for two populations?
  2. Is it necessary to use --rrate flag, since I don't really know the recombination rates?

Meanwhile, i also tried to install xpclr (Chen et al 2010), I am wondering that how can I create hapmapinput files, just to confirm are these files same as the plink output (.geno) files? For example, a vcf file from wild beets is my reference population (hapmapinput1) and from cultivated sugar beets is object population (hapmap2) or vice versa. If so, then may I ask how to create a mapInput file?

Kind regards, Amar

XiaXiaTianTian commented 1 year ago

Hi，Amar! Have you solved this? Is there any possibility that we can use xpclr when we don't know the recombination rate? All the best, Xia

Jiangjiangzhang6 commented 1 year ago

Hi，Amar! Have you solved this? Is there any possibility that we can use xpclr when we don't know the recombination rate? All the best, Xia

this software maybe no answer . I also meet the error for expclr .but just the person who asked , no one answer