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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Convert2Annovar produces empty file? #76

Closed vymao closed 5 years ago

vymao commented 5 years ago

Hi,

I have some vcf files for WES data that I wanted to run through Convert2Annovar, because I would like a csv output. However, I am getting a 0B file for this command:

/home/mk446/bin/annovar/convert2annovar.pl -format 'vcf4' 'combined.vcf' -outfile 'combined.avinput' -allsample

I'm not sure why. When I run Annovar, it doesnt seem like there's any error too. Does anyone know what is going on?

kaichop commented 5 years ago

Do not use convert2annovar. If you have a VCF file, just use table_annovar to annotate it. It can generate tab delimited or csv output.

On Mon, Oct 21, 2019 at 11:10 PM Victor notifications@github.com wrote:

Hi,

I have some vcf files for WES data that I wanted to run through Convert2Annovar, because I would like a csv output. However, I am getting a 0B file for this command:

/home/mk446/bin/annovar/convert2annovar.pl -format 'vcf4' 'combined.vcf' -outfile 'combined.avinput' -allsample

I'm not sure why. When I run Annovar, it doesnt seem like there's any error too. Does anyone know what is going on?

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vymao commented 5 years ago

How do I specify a csv output with a vcf file? If I use -vcfinput and -csvoutput it gives me an error?

Error in argument: -csvout is not compatible with -vcfinput

kaichop commented 5 years ago

There are two ways: (1) you can just generate a text output, and convert it to CSV file using a script, or using any software such as Excel (2) when you run table_annovar.pl you will see the correct command for running convert2annovar, and you will have the avinput file as a temporary file, so you can just annotate this intermediate file with -csvout and table_annovar.