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
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
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
Usage: Rscript ./input.vcf
Options: None
output: Fig of density Of Snps On cotton Chromosomes as output file automatically and a table
Usage: perl Change_phylip_tree_name.pl name.txt phylip.tree