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WGLab / InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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if there is vcf file have been annotated, how to skip the annotation step by annovar ? #33

Open cr01230 opened 6 years ago

cr01230 commented 6 years ago

we have been annotated the vcf, and then we run "python /opt/Intervar.py -b hg19 -i /opt/annovar.hg19_multianno.vcf --input_type=VCF -o out.vcf " there show error and dose't work. I really need to know how to used it after annotated vcf

quanliustc commented 6 years ago

Please add the option

--skip_annovar

Then you can use the annotation result for Intervar.

Quan LI, Ph.D

mailto:leequan@gmail.com leequan@gmail.com

mailto:Quan.Li@uhnresearch.ca Quan.Li@uhnresearch.ca

http://www.quanli.tk http://www.quanli.tk

From: MatthewCheng [mailto:notifications@github.com] Sent: Friday, September 07, 2018 4:18 AM To: WGLab/InterVar InterVar@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [WGLab/InterVar] if there is vcf file have been annotated, how to skip the annotation step by annovar ? (#33)

we have been annotated the vcf, and then we run "python /opt/Intervar.py -b hg19 -i /opt/annovar.hg19_multianno.vcf --input_type=VCF -o out.vcf " there show error and dose't work. I really need to know how to used it after annotated vcf

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shanbio commented 5 years ago

I tried with an annotated VCF file (annotation was done using Ensembl VeP) using below cmd:

python Intervar.py -b hg19 -i ~/TSVC2_annotated.vcf --input_type=VCF --skip_annovar -t intervardb -o output

The idea was not to invoke annovar and get it running using VeP annotation but it gives below errors.

ERROR: The InterVar did not find the annotation result file from ANNOVAR! ERROR: The name of annotation result file should be like output*.hg19__multianno.txt

Please Help ...

Habush commented 4 years ago

Did you get any solution? Currently having similar issue

EugeneEA commented 4 years ago

Did you get any solution? Currently having similar issue

Hi, I'm also trying to use VEP output with InterVar, but have no luck so far (and I realy do not want to write a "converter" of VEP output to Annovar output). Did you solve the issue somehow?

nliorni commented 3 years ago

Any solutions? I'm having the same problem with a vcf coming from a SnpEff/SnpSift Annotation and I get the same errors as @shanbio.