Question: annovar continues to use hg18 version despite using buildver hg19 argument
gravatar for dharaawasthi
25 days ago by
Indian Institute of Technology, Jodhpur
dharaawasthi0 wrote:

Hey, I am using ANNOVAR. I downloaded the required databases and entered the following command : $ perl <ceu.low_coverage.2010_10.indel.sites.vcf> --outfile final –buildverhg19 --protocol cytoBand,1000g2014oct_eur,1000g2014oct_afr,exac03,ljb26_all,clinvar_20140929,snp138 --operation r,f,f,f,f,f,f --vcfinput

I get the following ERROR despite including the buildverhg19 argument.

NOTICE: the --buildver argument is set as 'hg18' by default NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior) Error: the required database file –buildverhg19/hg18_cytoBand.txt does not exist.

I don't know why it is still using hg18 version.. Please help!!!!

annotation annovar 1000g • 86 views
ADD COMMENTlink written 25 days ago by dharaawasthi0

Please, use the appropriate format text. As I can identify, you just need a space on the -buildver option:

$ perl <ceu.low_coverage.2010_10.indel.sites.vcf> --outfile final –buildver hg19 --protocol cytoBand,1000g2014oct_eur,1000g2014oct_afr,exac03,ljb26_all,clinvar_20140929,snp138 --operation r,f,f,f,f,f,f --vcfinput
ADD REPLYlink modified 25 days ago • written 25 days ago by brunobsouzaa360
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