mingyue-mingyue / GWAS_script

Working on cotton resequencing

GWAS_script

1 Visualization_sweep_region.pl

visualization Fst and pi in cotton chrom. Usage: perl $0 [options]

Options:

    -Fst        : Fst generated by vcftools      
    -Pi_group1   : Pi generated by vcftools       
    -Pi_group2   : Pi generated by vcftools

output: Creat Table and Figure of the top 1%, 5% sweep_region in cotton genome as output file automatically

require R Package ggplot2 and qqman The version of cotton: Huyan et.al Nature genetic 2018

2 Call snp on RNA seq data.pl

Usage: perl $0 [options]

Options:

    -sample        <s> : list of sample name, ${sample_name}.R1.clean.fastq.gz
    -ref            <s> : reference genome for mapping used hista2 index file, fasta [pwd]
    -gtf            <s> : gene transcription file [pwd]
    -thread         <i> : numters of thread to use [4]
    -bam          <i>: 0 , bam keeped; 1 ,bam will be deleted

require picard(V1.124),gatk(v-4.1.0.0),STAR(2.7.0d_0221)，samtools（V1.6） output: Creat VCF file generated by GATK 4.0 as output file automatically

3 Stat_missing_ratio_on_vcf.r

Usage: Rscript ./out.imiss The out.imiss generated by vcftools (vcftools --gzvcf input.vcf ) Options: None output: Fig of missing ratio of 3 population cotton as output file automatically

4 Plotting Density Of Snps On Chromosomes.r

Usage: Rscript ./input.vcf

Options: None

output: Fig of density Of Snps On cotton Chromosomes as output file automatically and a table

5 Change_phylip_tree_name.pl

Usage: perl Change_phylip_tree_name.pl name.txt phylip.tree