Tumor
癌症序列变异解释和报告的标准和指南(ASCO和CAP联合推荐)
肺癌分析插件Can_28修复问题
Chom化疗插件及bug修复
Brca插件
FACTERA-fusionGene
SEGF-挖掘NGS中融合基因的新方法
maftools-肿瘤突变数据可视化神器
从数据库中获取免疫相关基因(IRGs)
数据库10KIP—基于ImmPort免疫组学数据挖掘
TCGA数据分析
下载分析TCGA数据库的数据
差异表达分析(limma & edgeR & DESeq2)
TCGA数据的规律【更新中】
生存分析
生存模型构建
突变数据
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Brca插件
## 1、分析流程 (1)path/myscript/get_brca_bam.pl从下机目录的ion_params_00.json文件来获取Brca的样本,并软链接到rawdata目录中。并通过size.pl程序对下机的bam文件大小判断是否位于160M到1.2G之间,从而得知定量是否有问题。下面(2)-(7)步在Shell目录中的shell脚本运行; (2)tmap进行比对,由于使用的是fasta文件仅有BRCA1/2基因的/results/plugins/Brca/BRCA_ref/BRCA1_2.fasta,因此比对之后需要通过程序alter_coordinate.pl对bam文件中表头和比对信息做校正(@HD条目改为unsorted、@SQ条目修改染色体长度LN,每一条比对的read信息中第三列position改成在基因组中的坐标位置)。不直接比对基因组的原因是这样比较快速吧。之后进行sort,index,获得如IonXpress_039_rawlib.bam名称的bam文件;对bam文件做基本统计(bamcheck程序,有GC含量等信息)。对bam文件进行countreads 和Q20 统计。 (3)对reads进行接头引物(primer_trimming.pl),生成修剪后的IonXpress_039_TRIM.bam文件(未细看)。之后进行index; (4)通过samtools mpileup和mpileupAnalysis.pl程序对bed区间(/results/plugins/Brca/design/BRCA1_2.20131001.noh.bed)分析生成mpileup格式并分析候选SNV,得到结果文件BamStat/mpileup/IonXpress_039.mppana.txt; (5)TVC检测变异(/results/plugins/Brca/design/BRCA1_2.merge.exon.bed),获得TVC/IonXpress_039/TSVC_variants.vcf文件; (6)对检出的vcf依据mpileup进行splitVcfMuliAlt.pl,结果输出到TVC/IonXpress_039/TSVC_variants_split.vcf并链接到TvcVcf/IonXpress_039.tvc.vcf,并将低质量的变异输出在plugin.outpath/lowquality_re.txt文件中; **因此需要添加未被TVC检出的位点,并到最后报告里。需要在这儿TSVC_variants_split.vcf加入,(信息可以依据mppana.txt结果写)** (7)ANNOVAR注释并转换为hgvs格式(TransFmt2hgvs.pl);通过trans_4bp_exon_junc.pl将注释结果文件的Func.refGene列为“exonic;splicing”且该位点在文件/results/plugins/Brca/design/BRCA1_2.junctions.exon.4bp.txt中,则Func.refGene列修改为“exonic”;输出结果文件:IonXpress_039.hg19_multianno.update.txt; (8)launch.sh中继续运行后续步骤(**已改成生成脚本mainwork.sh,方便以后修改致病性重新上传结果时可以一键运行**)。对BAM统计DepthOfCoverage,reads cov,以及PerSample的TargetRegion Depth Distribution,PerIntervals Depth Dis和Cumulate Depth Dis And Rplot等等;(**具体统计脚本未细看**); (9)所有变异的统计;获取该run的tvcvcf.list,avinput.list,multianno.list,进行所有样品变异结果的合并; 。。。。。 ``` echo "==== TMAP start at: `date +%Y-%m-%d%t%H:%M:%S` ====" tmap mapall -f /results/plugins/Brca/BRCA_ref/BRCA1_2.fasta -r /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/rawdata/IonXpress_039_rawlib.basecaller.bam -v -Y -u -o 2 -s /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039.tmap.bam stage1 map4 perl /results/plugins/Brca/myscript/alter_coordinate.pl /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039.tmap.bam /results/plugins/Brca/BRCA_ref/region /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039.tmap.new.bam samtools sort /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039.tmap.new.bam /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_rawlib samtools index /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_rawlib.bam echo "====TMAP and sort end at: `date +%Y-%m-%d%t%H:%M:%S` ====" echo "==== mpileup and bamcheck start at: `date +%Y-%m-%d%t%H:%M:%S` ====" /results/plugins/Brca/bin/bamcheck /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_rawlib.bam > /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/BamStat/Check/IonXpress_039.check echo "====bamcheck end at: `date +%Y-%m-%d%t%H:%M:%S` ====" echo "====countreads and Q20 start at: `date +%Y-%m-%d%t%H:%M:%S` ====" java -Xmx1g -jar /results/plugins/Brca/bin/jar/GenomeAnalysisTK.jar -T CountReads -R /results/plugins/Brca/BRCA_ref/ref.fasta -L /results/plugins/Brca/design/BRCA1_2.20131001.noh.exon.interval_list -I /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_rawlib.bam > /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/BamStat/CountReads/IonXpress_039.tgnrds # ref_new replace ref_hg19 perl /results/plugins/Brca/myscript/extraQ_bam.pl /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_rawlib.bam 20 > /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/BamStat/Q20/IonXpress_039.Q20.txt samtools index /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_rawlib.bam echo "==== countreads and Q20 end at: `date +%Y-%m-%d%t%H:%M:%S` ====" echo "====Primer Trimming start at: `date +%Y-%m-%d%t%H:%M:%S` ====" perl /results/plugins/Brca/myscript/primer_trimming.pl /results/plugins/Brca/design/pool_ampln.insert_rgn.txt.chr /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_rawlib.bam /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_TRIM.bam samtools index /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_TRIM.bam echo "====Primer Trimming end at: `date +%Y-%m-%d%t%H:%M:%S` ====" /results/plugins/Brca/bin/samtools mpileup -BQ0 -d 1000000 -f /results/referenceLibrary/tmap-f3/hg19/hg19.fasta /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_TRIM.bam -l /results/plugins/Brca/design/BRCA1_2.20131001.noh.bed > /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/BamStat/mpileup/IonXpress_039.mpp.txt perl /results/plugins/Brca/myscript/mpileupAnalysis.pl /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/BamStat/mpileup/IonXpress_039.mpp.txt /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/BamStat/mpileup/IonXpress_039.mppana.txt echo "==== mpileup end at: `date +%Y-%m-%d%t%H:%M:%S` ====" echo "====TVC start at: `date +%Y-%m-%d%t%H:%M:%S` ====" python /results/plugins/Brca/bin/variantCaller/variant_caller_pipeline.py -b /results/plugins/Brca/design/BRCA1_2.merge.exon.bed -i /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TMAP/IonXpress_039_TRIM.bam -r /results/plugins/Brca/BRCA_ref/ref.fasta -o /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039 -p /results/plugins/Brca/design/BRCA_pgm_4.0_20130920_parameters.json -B /results/plugins/Brca/bin/variantCaller echo "====TVC end at: `date +%Y-%m-%d%t%H:%M:%S` ====" perl /results/plugins/Brca/myscript/splitVcfMuliAlt.pl /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/TSVC_variants.vcf /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/TSVC_variants_split.vcf /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/BamStat/mpileup/IonXpress_039.mppana.txt /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/lowquality_re.txt ln -sf /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/TSVC_variants_split.vcf /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TvcVcf/IonXpress_039.tvc.vcf echo "====Annovar start at: `date +%Y-%m-%d%t%H:%M:%S` ====" perl /results/plugins/Brca/bin/annovar_edit/convert2annovar.pl -format vcf4 /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/TSVC_variants_split.vcf > /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/IonXpress_039\.avinput perl /results/plugins/Brca/bin/annovar_edit/table_annovar.pl /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/IonXpress_039\.avinput /results/plugins/Brca/annovardb/Chp2_BRCA_humandb --polish -buildver hg19 -protocol refGene,avsnp150,1000g2015aug_all,1000g2015aug_eas,exac03nontcga,dbnsfp33a,cosmic81,clinvar_20170905 -operation g,f,f,f,f,f,f,f -nastring - --argument "--exonicsplicing -splicing_threshold 2,,,,,,," --argument "-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs" --remove --outfile /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/IonXpress_039 perl /results/plugins/Brca/bin/annovar_edit/TransFmt2hgvs.pl -r /results/plugins/Brca/annovardb/Chp2_BRCA_humandb/hg19_refGene.txt -i /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/IonXpress_039.hg19_multianno.txt -o /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/IonXpress_039.hg19_multianno.intro.txt perl /results/plugins/Brca/myscript/trans_4bp_exon_junc.pl /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/IonXpress_039.hg19_multianno.intro.txt /results/plugins/Brca/design/BRCA1_2.junctions.exon.4bp.txt /results/analysis/output/Home/Auto_user_2456177-5-0049-127-P5-HiQ-pooling-Can28-BRCA-CHP2-20180927-ST_265_275/plugin_out/Brca_out.639/TVC/IonXpress_039/IonXpress_039.hg19_multianno.update.txt echo "====Annovar end at: `date +%Y-%m-%d%t%H:%M:%S` ====" ``` ## 2、关于致病性解读流程(脚本文件pathogenic_classfication.pl) 其中,定义致病性为risk。(最后画个流程图) (1)有害性预测 predict(良性benign,有害damage),8个预测软件统计,如damage>=4,则predict=“Damage”;如benign>=4,则predict=“Benign”。 (2)如果是无义突变(Nonsense)或者移码突变(frameshift): - 当Clinvar判断为“Uncertain_significance”、“Benign”、“Likely_benign" 或者 BIC_Info判断为Class1或Class2 或者 最大人群频率>=0.05 时,则risk为“unknown”(VUS); - 当Clinvar为'Likely_pathogenic' 或者 BIC_Info 判断为Class4 时, risk为“Likely pathogenic”; - 其他则为“pathogenic”; (3)如果是剪切位点突(Splicing)变或者错义突变(Missense),且人群频率低于0.05: - 当Clinvar 为'Pathogenic' 或者 BIC_Info为Class5时,risk为“pathogenic”; - 当Clinvar 为'Likely_pathogenic' 或者 BIC_Info为Class4时,risk为“Likely pathogenic”; - 当Clinvar 为'Benign' 或者 BIC_Info为Class1时,risk为“Benign”; - 当Clinvar 为'Likely_benign' 或者 BIC_Info为/Class2/时,risk为“likely benign”; - 当Clinvar 为'Uncertain_significance' 时,risk为“unknown”; - 当predict 判断为'Damage' 或者 BIC_Info为Pending时,risk为“unknown”; - 其他情况,则risk为“unknown”; (4)如果是剪切位点突(Splicing)变或者错义突变(Missense),且人群频率>=0.05: - 当Clinvar 为'Pathogenic' 或者 BIC_Info为Class5时,risk为“unkonwn”; - 当Clinvar 为'Likely_pathogenic' 或者 BIC_Info为Class4时,risk为“unkonwn”; - 当Clinvar 为'Benign' 或者 BIC_Info为Class1时,risk为“Benign”; - 当Clinvar 为'Likely_benign' 或者 BIC_Info为/Class2/时,risk为“likely benign”; - 当Clinvar 为'Uncertain_significance' 时,risk为“unknown”; - 其他情况,则risk为“benign”; (5)如果非移码突变(nonframeshift): - 当Clinvar 为'Pathogenic' 或者 BIC_Info为Class5时,risk为“pathogenic”; - 当Clinvar 为'Likely_pathogenic' 或者 BIC_Info为Class4时,risk为“likely pathogenic”; - 当Clinvar 为'Benign' 或者 BIC_Info为Class1时,risk为“Benign”; - 当Clinvar 为'Likely_benign' 或者 BIC_Info为/Class2/时,risk为“likely benign”; - 最大人群频率>= 0.05且 predict预测为 'Benign',则risk为“likely benign”; - 其他情况,则risk为“unknown”; (6)如果是同义突变(Synonymous),且最大人群频率低于0.01: - 当Clinvar判断为“Pathogenic”或“Likely_pathogenic”,或者BIC_Info为Class5或Class4时,则risk判断为“unknown”; (7)如果是其他突变(非以上所列突变类型): - 当Clinvar 为'Pathogenic' 或者 BIC_Info为Class5时,risk为“pathogenic”; - 当Clinvar 为'Likely_pathogenic' 或者 BIC_Info为Class4时,risk为“likely pathogenic”; - 当人群频率高于0.05,且Clinvar 为'Benign' 或者 BIC_Info为Class1时,risk为“Benign”; - 当人群频率高于0.05,且Clinvar 为'Likely_benign' 或者 BIC_Info为/Class2/时,risk为“likely benign”; - 其他情况,则risk为“unknown”; 3、前端报告系统展示时,在前端也是有进行过过滤的。 ## Brca插件BUG修复:  1、首先要修改上面的致病性解读流程,修改后在更新过的pathogenic_classfication_new.pl脚本中。(P5 /results/analysis/output/Home/lhlv/Tumor/Brca_anno_pathogenic目录中) 2、更新clinvar数据库,最新为20181202(注意/results/plugins/Brca/design/目录和/results/plugins/Brca/annovardb/Chp2_BRCA_humandb/目录中版本不同,需要确认下) 3、对应到clinvar的两个参数:CLNSIG和CLNREVSTAT修改脚本extractVarAnnoBrca_new.pl。参考资源为:https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 和 https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/ ## BRCA校准计划 将test.vcf文件放入rawdata目录中,然后运行下面test.sh即可。 ``` mkdir newdata; mkdir result cnt=0 for i in `ls rawdata|grep vcf`;do cnt=$((${cnt}+1)) echo $i IonXpress_${cnt} >> barcode2sample.txt grep -v '^Chr' rawdata/$i|awk -v OFS="\t" '{if($5=="hom"){print $1,$2,".",$3,$4,".","PASS",".","GT","1/1"}else{print $1,$2,".",$3,$4,".","PASS",".","GT","0/1"}}' > newdata/IonXpress_${cnt}.tvc.vcf perl /results/plugins/Brca/bin/annovar_edit/convert2annovar.pl -format vcf4 newdata/IonXpress_${cnt}.tvc.vcf > result/IonXpress_${cnt}.avinput perl /results/plugins/Brca/bin/annovar_edit/table_annovar.pl result/IonXpress_${cnt}.avinput /results/plugins/Brca/annovardb/Chp2_BRCA_humandb --polish -buildver hg19 -protocol refGene,avsnp150,1000g2015aug_all,1000g2015aug_eas,exac03nontcga,dbnsfp33a,cosmic81,clinvar_20170905 -operation g,f,f,f,f,f,f,f -nastring - --argument "--exonicsplicing -splicing_threshold 2,,,,,,," --argument "-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs" --remove --outfile result/IonXpress_${cnt} perl /results/plugins/Brca/bin/annovar_edit/TransFmt2hgvs.pl -r /results/plugins/Brca/annovardb/Chp2_BRCA_humandb/hg19_refGene.txt -i result/IonXpress_${cnt}.hg19_multianno.txt -o result/IonXpress_${cnt}.hg19_multianno.intro.txt perl /results/plugins/Brca/myscript/trans_4bp_exon_junc.pl result/IonXpress_${cnt}.hg19_multianno.intro.txt /results/plugins/Brca/design/BRCA1_2.junctions.exon.4bp.txt result/IonXpress_${cnt}.hg19_multianno.update.txt done :<<efo perl /results/plugins/Brca/bin/annovar_edit/convert2annovar.pl -format vcf4 newdata/IonXpress_001.tvc.vcf > result/IonXpress_001.avinput perl /results/plugins/Brca/bin/annovar_edit/table_annovar.pl result/IonXpress_001.avinput /results/plugins/Brca/annovardb/Chp2_BRCA_humandb --polish -buildver hg19 -protocol refGene,avsnp150,1000g2015aug_all,1000g2015aug_eas,exac03nontcga,dbnsfp33a,cosmic81,clinvar_20170905 -operation g,f,f,f,f,f,f,f -nastring - --argument "--exonicsplicing -splicing_threshold 2,,,,,,," --argument "-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs" --remove --outfile result/IonXpress_001 perl /results/plugins/Brca/bin/annovar_edit/TransFmt2hgvs.pl -r /results/plugins/Brca/annovardb/Chp2_BRCA_humandb/hg19_refGene.txt -i result/IonXpress_001.hg19_multianno.txt -o result/IonXpress_001.hg19_multianno.intro.txt perl /results/plugins/Brca/myscript/trans_4bp_exon_junc.pl result/IonXpress_001.hg19_multianno.intro.txt /results/plugins/Brca/design/BRCA1_2.junctions.exon.4bp.txt result/IonXpress_001.hg19_multianno.update.txt efo ls newdata/*.tvc.vcf > tvcvcf.list avinput_list="avinput.list" ls result/*.avinput > ${avinput_list} multi_list="multianno.list" ls result/*.hg19_multianno.update.txt > ${multi_list} perl /results/plugins/Brca/myscript/MergeVcfTools.pl tvcvcf.list allvar.vcf perl /results/plugins/Brca/myscript/extractInfoTvcVcf.pl allvar.vcf allvar.info #perl /results/plugins/Brca/myscript/extractVarAnnoBrca.pl avinput.list multianno.list allvar.info allanno.txt perl /results/plugins/Brca/myscript/extractVarAnnoBrca_new.pl avinput.list multianno.list allvar.info allanno.txt perl /results/plugins/Brca/myscript/addHgmdbicForAnno.pl allanno.txt /results/plugins/Brca/design/BRCA1_2_BIC.txt /results/plugins/Brca/design/hgmd.brca2013.txt allanno_hgmd_bic_clin.txt /results/plugins/Brca/design/FP.pos perl /results/plugins/Brca/myscript/pathogenic_classfication_new.pl allanno_hgmd_bic_clin.txt allanno_hgmd_bic_clin_final.txt python /results/plugins/Brca/myscript/bug_fixer/splicing_fixer.py allanno_hgmd_bic_clin_final.txt #cut -f 112 allanno_hgmd_bic_clin_final.txt #for i in `ls newdata/*.vcf`;do awk 'BEGIN{a=0}{if($2-a==1){print FILENAME"\n"b"\n"$0};b=$0;a=$2}' $i;done #egrep -w 'IonXpress_1380|IonXpress_1384|IonXpress_2061|IonXpress_20' barcode2sample.txt #15B0027546.BRCA.vcf IonXpress_20 #BC-011.BRCA.vcf IonXpress_1380 #BC-015.BRCA.vcf IonXpress_1384 #NF92.BRCA.vcf IonXpress_2061 #AN00004.BRCA.vcf IonXpress_1260 #AN00072.BRCA.vcf IonXpress_1326 ```
laihui126
2023年1月9日 14:32
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