{"id":611,"date":"2025-07-14T10:13:50","date_gmt":"2025-07-14T02:13:50","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=611"},"modified":"2025-07-14T11:28:15","modified_gmt":"2025-07-14T03:28:15","slug":"pyclone-vi-%e8%be%93%e5%85%a5%e6%96%87%e4%bb%b6%e5%a4%84%e7%90%86","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2025\/07\/14\/pyclone-vi-%e8%be%93%e5%85%a5%e6%96%87%e4%bb%b6%e5%a4%84%e7%90%86\/","title":{"rendered":"Pyclone-vi \u8f93\u5165\u6587\u4ef6\u5904\u7406"},"content":{"rendered":"

1. Call Somatic Mutations<\/h3>\n

\u9996\u5148\u901a\u8fc7Mutect2\u3001Varscan2\u3001Strelka2\u7b49\u83b7\u53d6\u6837\u672c\u7a81\u53d8maf\u6587\u4ef6\uff0c\u8fc7\u6ee4\u540e\u5408\u5e76\uff0c\u83b7\u53d6\u6700\u7ec8maf\u6587\u4ef6\uff0c<\/p>\n

# R\n# \u9700\u8981\u4fee\u6539\u8fc7\u6ee4\u540e\u7684maf\u6587\u4ef6\u7684Tumosamplebarcode\uff0c\u628a\u7528\u4e8e\u6784\u5efa\u8fdb\u5316\u7684\u6837\u672c\u6539\u6210\u4e00\u6837\u7684Tumosamplebarcode\nMerged_maf_df <- read.table("\/Users\/zhoukaiwen\/Desktop\/Breast_Phyllodes_Tumor\/Bioinfo\/WES\/Mutation\/6patients_mutect2_varscan2_intersect_pass.Somatic.hc.hg38_multianno_filtered.maf",\n                            header = T,sep = '\\t',quote = "")\n\ntable(Merged_maf_df$Tumor_Sample_Barcode)\n# \u76f4\u63a5\u5220\u9664-BNPT\u548c-FA\uff0c\u83b7\u53d6\u5355\u72ec\u4ee5-M\u548c-E\u533a\u5206\u7684Tumor_Sample_Barcode\nMerged_maf_df$Tumor_Sample_Barcode <- gsub("-BNPT","",Merged_maf_df$Tumor_Sample_Barcode)\nMerged_maf_df$Tumor_Sample_Barcode <- gsub("-FA","",Merged_maf_df$Tumor_Sample_Barcode)\ntable(Merged_maf_df$Tumor_Sample_Barcode)\n\nwrite.table(Merged_maf_df,"\/Users\/zhoukaiwen\/Desktop\/Breast_Phyllodes_Tumor\/Bioinfo\/WES\/Mutation\/6patients_mutect2_varscan2_intersect_pass_Tumor_Sample_Barcode_merged.Somatic.hc.hg38_multianno_filtered.maf",col.names = T,row.names = F,sep = '\\t',quote = F)\n<\/code><\/pre>\n
2. \u5c06\u4fee\u6574\u8fc7\u7684maf\u6587\u4ef6\u8f6c\u6362\u4e3avcf\u6587\u4ef6(\u6839\u636eT-N\u8fdb\u884c\u62c6\u5206)<\/h3>\n
maf2vcf.pl --input-maf 6patients_mutect2_varscan2_intersect_pass_Tumor_Sample_Barcode_merged.Somatic.hc.hg38_multianno_filtered.maf --output-dir \/groups\/phyllodes\/home\/share\/Results\/WES\/maf2vcf --output-vcf 6patients_mutect2_varscan2_intersect_pass_Tumor_Sample_Barcode_merged --ref-fasta \/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa --per-tn-vcfs<\/code><\/pre>\n
3. \u4f7f\u7528gatk ASEReadCounter\u63d0\u53d6allele specific\u4f4d\u70b9\u4fe1\u606f\uff08\u4e0d\u51c6\uff09<\/h3>\n
\u6ce8\u610f\u6b64\u5904\u7684sample_pair.txt\u8981\u52a0\u591a\u7b2c\u56db\u5217\u4e3a\u5206\u7ec4\u4fe1\u606f<\/p>\n
perl -ne 'chomp; next if \/^$\/; @a = split \/\\t\/; print "bcftools sort $a[3]\\_vs\\_$a[1].vcf -o $a[3]\\_vs\\_$a[1].sorted.vcf && gatk IndexFeatureFile -I $a[3]\\_vs\\_$a[1].sorted.vcf && gatk ASEReadCounter -R ~\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa -I ..\/align\/$a[0]_bqsr.bam -V $a[3]\\_vs\\_$a[1].sorted.vcf -L ~\/database\/AgilentV6_GRCh38_ex_region.sort.filtered.bed --min-base-quality 10 --min-mapping-quality 20 -O $a[0].shared.sites.vcf && echo $a[0] ASEReadCounter ok\\n"' sample_pair.txt > ASEReadCounter.sh<\/code><\/pre>\n
3. \u91cd\u8dd1gatk Mutect2\uff0c\u8bbe\u5b9aforce call\uff0c\u83b7\u53d6\u6307\u5b9a\u4f4d\u70b9\u7684\u4fe1\u606f<\/h3>\n
\u6ce8\u610f--allele\u548c-L\u53c2\u6570\u90fd\u8981\u6307\u5b9a\u4e3a\u4e0a\u4e00\u6b65\u6784\u5efa\u7684vcf\u6587\u4ef6\uff0c\u624d\u80fd\u6307\u5b9a\u4f4d\u70b9force-call
\n\u6ce8\u610f\u6b64\u5904\u7684sample_pair.txt\u8981\u52a0\u591a\u7b2c\u56db\u5217\u4e3a\u5206\u7ec4\u4fe1\u606f<\/p>\n
perl -ne 'chomp; next if \/^$\/; @a = split \/\\t\/; print "bcftools sort $a[3]\\_vs\\_$a[1].vcf -o $a[3]\\_vs\\_$a[1].sorted.vcf && gatk IndexFeatureFile -I $a[3]\\_vs\\_$a[1].sorted.vcf && gatk Mutect2 -R ~\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa -I ..\/align\/$a[0]_bqsr.bam -I ..\/align\/$a[1]_bqsr.bam -tumor $a[0] -normal $a[1] --alleles $a[3]\\_vs\\_$a[1].sorted.vcf -L $a[3]\\_vs\\_$a[1].sorted.vcf --germline-resource ~\/database\/gatk_bundle\/hg38\/somatic-hg38_af-only-gnomad.hg38.vcf.gz -pon ~\/database\/gatk_bundle\/hg38\/somatic-hg38_1000g_pon.hg38.vcf.gz --f1r2-tar-gz $a[0].shared.sites.f1r2.tar.gz -O $a[0].shared.sites.raw.vcf && echo $a[0] Mutect2 force call ok\\n"' sample_pair.txt > Mutect2_force_call_short.sh<\/code><\/pre>\n
4. vcf2maf \u8f6c\u6362\u4e3amaf<\/h3>\n
perl -ne 'chomp;next if($_=~\/^$\/);my @a=split \/\\t\/;print "vcf2maf.pl --input-vcf $a[0].shared.sites.raw.vcf --output-maf $a[0].shared.sites.maf --normal-id $a[1] --tumor-id $a[0] --vcf-tumor-id $a[0] --vcf-normal-id $a[1] --vep-path \/home\/zhoukaiwen\/software\/anaconda3\/envs\/vcf2maf\/bin --vep-data \/home\/zhoukaiwen\/database\/vep\/ --ref-fasta \/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa --verbose --ncbi-build GRCh38 --cache-version 114 && echo $a[0] vcf2maf ok\\n"' sample_pair.txt >vcf2maf.sh\n\n# \u5408\u5e76maf\ncat *.shared.sites.maf | egrep "^#|^Hugo_Symbol" | head -2 > 6patients.shared.sites.maf\ncat *.shared.sites.maf | egrep -v "^#|^Hugo_Symbol" >> 6patients.shared.sites.maf<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
1. Call Somatic Mutations \u9996\u5148\u901a\u8fc7Mutect2\u3001Varscan2\u3001Strelka2…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-611","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/611","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=611"}],"version-history":[{"count":5,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/611\/revisions"}],"predecessor-version":[{"id":616,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/611\/revisions\/616"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=611"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=611"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=611"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}