Shulou(Shulou.com)06/02 Report--

Today, I would like to introduce to you the annotation results of the vcf file annovar and the maftools example analysis of the waterfall diagram. The content of the article is good. Now I would like to share it with you. Friends who feel in need can understand it. I hope it will be helpful to you. Let's read it along with the editor's ideas.

The annotation result of vcf file annovar draws waterfall diagram and maftools analysis

1.vcf file annovar comments:

Table_annovar.pl 154.raw.somatic.vcf.gz humandb/hg38/-buildver hg38-out 154remove-protocol\ refGene,cosmic70,nci60,esp6500siv2_all,clinvar_20210501,1000g2015aug_all,1000g2015aug_eas,1000g2015aug_sas,avsnp150,gwasCatalog,ljb26_all,cytoBand,dgvMerged,phastConsElements100way,genomicSuperDups-operation g nastring. -vcfinput

two。 Extract the necessary information

For i in * .hg38_multianno.txt do sample= `echo $I | awk-F'.'{print $2} '`cut-f' 1-10' $I | sed '1d' | sed "1s/ 1s/ ^ / Chr\ tStart\ tEnd\ tRef\ tAlt\ tFunc.refGene\ tGene.refGene\ tGeneDetail.refGene\ tExonicFunc.refGene\ tAAChange.refGene\ tTumor_Sample_Barcode\ nCompact' all_sample.txt

3. Read in the data and draw with maftools

Library (maftools) var_maf= annovarToMaf (annovar = "all_sample.txt", Center = 'NA', refBuild =' hg38', tsbCol = 'Tumor_Sample_Barcode', table =' refGene',MAFobj = T Sep = "\ t") plotmafSummary (maf = var_maf, rmOutlier = TRUE, addStat = 'median') oncoplot (maf = var_maf, top = 30, fontSize = 12, showTumorSampleBarcodes = F) these are the annotations of the vcf file annovar and the whole content of the maftools example analysis of the waterfall diagram. For more information related to the vcf file annovar annotations, waterfall drawing, maftools instance analysis, you can search for previous articles or browse the following articles to learn! I believe the editor will add more knowledge to you. I hope you can support it!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.