8000 Input files requirement for XP-CLR · Issue #89 · hardingnj/xpclr · GitHub
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Input files requirement for XP-CLR #89

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dhimanamar opened this issue Dec 28, 2022 · 2 comments
Open

Input files requirement for XP-CLR #89

dhimanamar opened this issue Dec 28, 2022 · 2 comments

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@dhimanamar
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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
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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
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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

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@dhimanamar @XiaXiaTianTian @Jiangjiangzhang6
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