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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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table_annovar.pl 添加 HGVS 注释 #70

Closed solivehong closed 5 years ago

solivehong commented 5 years ago

你好 我发现annovar 的默认结果中并不是HGVS注释，请问如何输出参数才能获得hgvs注释的mutation 这是我输入的参数

perl /gpfs/home/zhaohongqiang/pipeline/pipe_bin/table_annovar.pl /gpfs/project/RD_bioinfor/WES_clinical/20190520_WES/zhangchunting_ffpe/annotation/reformed.PM2019042801.3tool.for_anno.vcf.gz /gpfs/software/pipeline/pipeline/database/annovar_humandb -buildver hg19 -remove -protocol refGene,cosmic70,avsnp147,esp6500siv2_all,exac03,1000g2015aug_all,1000g2015aug_eas,clinvar_20181028,dbnsfp30a -operation gh,f,f,f,f,f,f,f,f -nastring . -vcfinput -out /gpfs/project/RD_bioinfor/WES_clinical/20190520_WES/zhangchunting_ffpe/annotation/reformed.PM2019042801.3tool

期待您的回答

solivehong commented 5 years ago

还有一个问题是如何更改复杂突变的格式 比如p.7_8del 我见到网上有人注释成为 类似p.A7_G8del这个样子的

kaichop commented 5 years ago

You can use -argument to supply the "-hgvs" argument to the first annotation. -argument '-hgvs',,,,,,,,

Also add -polish to get more accurate annotation on indels such as A7_G8del.

On Mon, Jul 15, 2019 at 4:58 AM zhaohongqiangsoliva < notifications@github.com> wrote:

你好 我发现annovar 的默认结果中并不是HGVS注释，请问如何输出参数才能获得hgvs注释的mutation 这是我输入的参数

perl /gpfs/home/zhaohongqiang/pipeline/pipe_bin/table_annovar.pl /gpfs/project/RD_bioinfor/WES_clinical/20190520_WES/zhangchunting_ffpe/annotation/reformed.PM2019042801.3tool.for_anno.vcf.gz /gpfs/software/pipeline/pipeline/database/annovar_humandb -buildver hg19 -remove -protocol refGene,cosmic70,avsnp147,esp6500siv2_all,exac03,1000g2015aug_all,1000g2015aug_eas,clinvar_20181028,dbnsfp30a -operation gh,f,f,f,f,f,f,f,f -nastring . -vcfinput -out /gpfs/project/RD_bioinfor/WES_clinical/20190520_WES/zhangchunting_ffpe/annotation/reformed.PM2019042801.3tool

期待您的回答

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solivehong commented 5 years ago

请问我该如何写

kaichop commented 5 years ago

I said it below

-argument '-hgvs',,,,,,,,

and

-polish

On Tue, Jul 16, 2019 at 12:15 AM zhaohongqiangsoliva < notifications@github.com> wrote:

请问我改如何写

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solivehong commented 5 years ago

I downloaded the new version and entered it using the command below

perl ~/annovar/annovar_new/annovar/table_annovar.pl /gpfs/project/RD_bioinfor/WES_clinical/20190520_WES/zhangchunting_ffpe/annotation/PM2019042801.sofstric.watson.vcf /gpfs/software/pipeline/pipeline/database/annovar_humandb -buildver hg19 -remove -protocol refGene,cosmic70,avsnp147,esp6500siv2_all,exac03,1000g2015aug_all,1000g2015aug_eas,clinvar_20160302,dbnsfp30a -operation g,f,f,f,f,f,f,f,f -argument '-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs' -nastring . -vcfinput  -out /gpfs/project/RD_bioinfor/WES_clinical/20190520_WES/zhangchunting_ffpe/annotation/PM2019042801.sofstric.watson.hgvs.vcf -polish

but I still get the following results

NOS1AP:NM_001164757:exon8:c.886_888del:p.Q301del,NOS1AP:NM_014697:exon8:c.901_903del:p.Q306del
xiucz commented 5 years ago

@kaichop ，please have a look this problem, I am also interested in it. Thanks a lot.

kaichop commented 5 years ago

I said it below. The two arguments need to be used in table_annovar. zhaohongqiangsoliva did not follow my suggestion. But that specific output (one line) is already in HGVS format with cdot and pdot.

-argument '-hgvs',,,,,,,,

and

-polish

I will close this issue.

xiucz commented 5 years ago

thank you@kaichop I have got you, it works well now.