perl /share/nas1/yuj/pipline/pop-pip/v1.1/script/02variant/vcf_to_snplist_v1.4.pl -i /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/analysis/vcf_filter/samples.gatk.snp.m2M2.mis0.2.mac3.4dtv.vcf -o /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/core3/samples.gatk.snp.m2M2.mis0.2.mac3.4dtv.list -ref 1

配置文件:
cp /share/nas1/yuj/pipline/core_germplasm/v1.0/core_germ.yaml ./

主流程:
perl /share/nas1/yuj/pipline/core_germplasm/v1.0/core_germ_pip.pl -i core_germ.yaml -o analysis

整理结果:
perl /share/nas1/yuj/pipline/core_germplasm/v1.0/script/result/resultsdir.pl -i analysis/   -o complete_dir

报告:
cp /share/nas1/yuj/pipline/core_germplasm/v1.0/Web_Report/core_report.cfg ./

perl /share/nas1/yuj/pipline/core_germplasm/v1.0/Web_Report/core_Web_Report.pl -id complete_dir/  -cfg core_report.cfg

待修改部分

pca

同遗传进化 map文件的生成

vcf转list

perl /share/nas1/yuj/pipline/pop-pip/v1.1/script/02variant/vcf_to_snplist_v1.4.pl  -i  /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/analysis/vcf_filter/samples.gatk.snp.m2M2.mis0.2.mac3.4dtv.vcf   -o  /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/core3/samples.gatk.snp.m2M2.mis0.2.mac3.4dtv.list -ref 1 

绘图chrStat

/share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/core3/analysis/geno_stat/samples.chrStat.xls
要把第一列id缩短一下

绘图
Rscript /share/nas1/yuj/pipline/core_germplasm/v1.0/script/geno_stat/popSNPNumStat.r /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/core3/analysis/geno_stat/samples.chrStat.xls /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/core3/analysis/geno_stat/samples.chrStat.pdf  && convert -density 600 /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/core3/analysis/geno_stat/samples.chrStat.pdf /share/nas1/yuj/project/re-sequencing/GP-20230517-6067_20230621/core3/analysis/geno_stat/samples.chrStat.png