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：

![](/media/202301/2023-01-09_143144&5HwpqgKEIxZoM7vjNX0P.png)

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
```