跳至内容
售后
用户工具
登录
站点工具
搜索
工具
显示页面
修订记录
反向链接
最近更改
媒体管理器
网站地图
登录
>
最近更改
媒体管理器
网站地图
您的足迹:
疾病显著性关联基因分析_burden_skato
编辑本页后请点击“保存”。请参阅
syntax
了解维基语法。只有在您能
改进
该页面的前提下才编辑它。如果您想尝试一些东西,请先到
playground
热身。
媒体文件
======简介====== 基于基因的关联分析 ======功能====== 基于基因的关联分析(Burden) ======脚本使用====== **1. 配置文件:** <code> 合并后的snp注释文件 示例脚本step1:过滤SNP文件 echo "Filter snp start: " $(date) && \ python /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/VariantFilter.v1.4.4.py \ --in /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/snp.merged.annovar.hg19_multianno.xls.gz \ --func \ --sys \ --loss \ --sp 2 \ --freqli '1000g_ALL 0.005;GnomAD_ALL_AF 0.005;GnomAD_EAS_AF 0.005;NovoDb_WES 0.005' \ --dam P \ --gerp \ --repeat \ --out /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp && \ echo "Filter snp end: " $(date) 示例脚本step2:过滤indel文件 echo "Filter indel start: " $(date) && \ python /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/VariantFilter.v1.4.4.py \ --in /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/indel.merged.annovar.hg19_multianno.xls.gz \ --func \ --sys \ --loss \ --sp 2 \ --freqli '1000g_ALL 0.005;GnomAD_ALL_AF 0.005;GnomAD_EAS_AF 0.005;NovoDb_WES 0.005' \ --dam F \ --repeat \ --out /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.indel && \ echo "Filter indel end: " $(date) 示例脚本step3:卡bed区间 echo "Extract bed start: " $(date) && \ python /ifs/TJPROJ3/DISEASE/Database/ExAC/gnomAD/ExtractAgilentBed_only.py \ /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.func.sys.1000g_ALL.GnomAD_ALL_AF.GnomAD_EAS_AF.NovoDb_WES.repeat.deleterious.xls \ /ifs/TJPROJ3/DISEASE/Database/Exome_bed/Agilent/SureSelectXT.Human.All.Exon.V6/S07604514_Regions_extract.bed \ /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.func.sys.1000g_ALL.GnomAD_ALL_AF.GnomAD_EAS_AF.NovoDb_WES.repeat.deleterious.bed_only.xls && \ python /ifs/TJPROJ3/DISEASE/Database/ExAC/gnomAD/ExtractAgilentBed_only.py \ /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.indel.func.sys.1000g_ALL.GnomAD_ALL_AF.GnomAD_EAS_AF.NovoDb_WES.repeat.xls \ /ifs/TJPROJ3/DISEASE/Database/Exome_bed/Agilent/SureSelectXT.Human.All.Exon.V6/S07604514_Regions_extract.bed \ /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.indel.func.sys.1000g_ALL.GnomAD_ALL_AF.GnomAD_EAS_AF.NovoDb_WES.repeat.bed_only.xls && \ echo "Extract bed end: " $(date) 示例脚本step4:merge常染色体的snp和indel echo "Autosome and Merge SNP INDEL start: " $(date) && \ awk -F"\t" '{if ($2!="X" && $2!="Y") print}' /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.func.sys.1000g_ALL.GnomAD_ALL_AF.GnomAD_EAS_AF.NovoDb_WES.repeat.deleterious.bed_only.xls > /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.filtered.padded.autosome.xls && \ awk -F"\t" '{if ($2!="X" && $2!="Y") print}' /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.indel.func.sys.1000g_ALL.GnomAD_ALL_AF.GnomAD_EAS_AF.NovoDb_WES.repeat.bed_only.xls > /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.indel.filtered.padded.autosome.xls && \ cat /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.filtered.padded.autosome.xls /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.indel.filtered.padded.autosome.xls | sed -E "2,\${/Priority/d}" > /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.indel.filtered.padded.autosome.xls && \ echo "Autosome Merge SNP INDEL end: " $(date) 示例脚本step5:进行snp和indel的burden分析,计算P值等; echo "Burden snp start: " $(date) && \ python /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/GetBurdenFre_v1.6.py \ -case /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.filtered.padded.autosome.xls \ -control /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/NovoDb2827/Novo.2827.wes.snp.filterAgilentV6Pad100.stat.noXY.xls \ -cc N \ -Num 2827 \ -cr 0.95 \ -nr 0.6 \ -out /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.burden.snp.stat.xls && \ cd /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test && \ Rscript /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/GeneFisherPlot.R \ --infile S167.burden.snp.stat.xls \ --outpre S167.burden.snp && \ paste S167.burden.snp.fisher.xls S167.burden.snp.stat.samstat.xls |sort -g -k6> S167.burden.snp.fisher.sample.sorted.xls && \ echo "Burden snp end: " $(date):merge常染色体的snp和indel 示例脚本step56:进行snp的burden分析,计算P值等; echo "Burden snp start: " $(date) && \ python /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/GetBurdenFre_v1.6.py \ -case /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.snp.filtered.padded.autosome.xls \ -control /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/NovoDb2827/Novo.2827.wes.snp.filterAgilentV6Pad100.stat.noXY.xls \ -cc N \ -Num 2827 \ -cr 0.95 \ -nr 0.6 \ -out /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/S167.burden.snp.stat.xls && \ cd /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test && \ Rscript /ifs/TJPROJ3/DISEASE/share/Disease/Association/Burden/GeneFisherPlot.R \ --infile S167.burden.snp.stat.xls \ --outpre S167.burden.snp && \ paste S167.burden.snp.fisher.xls S167.burden.snp.stat.samstat.xls |sort -g -k6> S167.burden.snp.fisher.sample.sorted.xls && \ echo "Burden snp end: " $(date) </code> 运行脚本: <code> /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/work.sh sh 刷脚本; /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test/shell qsub投递; </code> ======交付结果====== burden的表格; 曼哈顿图; QQ图; 示例路径: /TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/Burden/test
保存
预览
取消
编辑摘要
当您选择开始编辑本页,即寓示你同意将你贡献的内容按下列许可协议发布:
CC Attribution-Share Alike 4.0 International
疾病显著性关联基因分析_burden_skato.txt
· 最后更改: 2023/03/31 06:12 由
hanyue
页面工具
显示页面
修订记录
反向链接
回到顶部