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This article introduces the knowledge of "how to use XP CLR to detect selection signals in the genome". In the operation of practical cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

Introduction to the method of preparing analytical documents:

If you do not know how to program, the input file of the above xpclr is not easy to prepare. Here we teach you to use plink to generate .geno files. Since xpclr can only run one chromosome at a time, here is an example of the first chromosome to run:

# # generate pop1 subgroup geno file # change the sample name into two columns to facilitate plink conversion and generate .geno file: awk'{print $1 "\ t" $1} 'pop1.txt > pop1.keep.txtplink-- vcf $workdir/00.filter/clean.sorted.vcf.gz\-- keep pop1.keep.txt-- chr 1-- out Chr1.pop1\-- recode 01 transpose-output-missing-genotype 9\-- allow-extra-chr -- set-missing-var-ids @: #-- keep-allele-ordercut-d ""-f 5-Chr1.pop1.tped | awk'{print $0 ""}'> Chr1.pop1.geno## generates the pop2 subgroup geno file awk'{print $1 "\ t" $1}'$datadir/pop2.txt > pop2.keep.txtplink-- vcf $workdir/00.filter/clean.sorted.vcf.gz\-- keep pop2.keep.txt-- chr 1 -- out Chr1.pop2\-- recode 01 transpose-output-missing-genotype 9\-- allow-extra-chr-- set-missing-var-ids @: #-- keep-allele-ordercut-d ""-f 5-Chr1.pop2.tped | awk'{print $0 ""}'> Chr1.pop2.geno## generates snp location information file zcat clean.sorted.vcf.gz | awk'$1 location = "1" {print "" $1 ":" $2 "\ tChr01\ t" $2CM100000000 "\ t" $2 "\ t" $4 "\ t" $5}'> Chr01.snp## run xpclr analysis XPCLR-xpclr Chr1.pop1.geno Chr1.pop2.geno Chr01.snp Chr01.out-w1 0.005 2000 Chr01-p0 0.95chromosome # replace chromosome name sed's / ^ 0 / Chr01/' Chr01.out.xpclr.txt

In the resulting result file, each column represents the calculated XP-CLR score of chr# grid# # ofSNPs_in_window physical_pos genetic_pos XPCLR_score max_s,XPCLR_score.

That's all for "how to use XP CLR to detect selection signals in the Genome". Thank you for reading. If you want to know more about the industry, you can follow the website, the editor will output more high-quality practical articles for you!

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