Hi,
I'm pretty new to bioinformatics.
I'm training on a set of 2 WES (whole exomes sequencing) to get introduced to all those steps.
I followed the GATK good practices, and I'm with a joint VCF file, and then I want to filter and annotate it with annovar.
Before working on annovar, I chose to convert vcf to avinput.
For that I tried the following :
And i have the following error (ubuntu 14.04 or 16.04) :
It's not about rights, my colleage bioinformatician looked it up with me, it's all about how convert2annovar deals with the argument -allsamples to get a outfile per sample.
Otherwise convert2annovar works fine to me.
The only workaround I found is to use the parameter "-withfreq" which makes it work like a charm..
I can't find anything on google, have you any ideas about where that error could come from?
Best,
I'm pretty new to bioinformatics.
I'm training on a set of 2 WES (whole exomes sequencing) to get introduced to all those steps.
I followed the GATK good practices, and I'm with a joint VCF file, and then I want to filter and annotate it with annovar.
Before working on annovar, I chose to convert vcf to avinput.
For that I tried the following :
convert2annovar.pl -format vcf4 -allsample input.vcf -outfile STDOUT
NOTICE: output files will be written to STDOUT.<samplename>.avinput
cannot write to outfile
cannot write to outfile
Otherwise convert2annovar works fine to me.
The only workaround I found is to use the parameter "-withfreq" which makes it work like a charm..
I can't find anything on google, have you any ideas about where that error could come from?
Best,
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