table_annovar.pl script shows error

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4.1 years ago

Dhara Awasthi ▴ 40

Hey I am using Annovar to analyse my multi sample vcf files I downloaded from 1000G. I am getting this error:

perl table_annovar.pl CEU.low_coverage.2010_10.indel.genotypes.vcf humandb/ -buildver hg19 -out myanno -remove -protocol 1000g2014oct_all -operation f -vcfinput

NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)

Error: the required database file humandb/hg19_ALL.sites.2014_10.txt does not exist.

FYI: I checked the humandb folder and it contains the hg19_ALL.sites.2014.txt

I don't know why it's showing error. PLEASE HELP!!!

annovar 1000g annotation • 1.9k views

ADD COMMENT • link updated 4.1 years ago by Kevin Blighe 88k • written 4.1 years ago by Dhara Awasthi ▴ 40

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Hi, can you confirm that you downloaded the database like this:

annotate_variation.pl -downdb 1000g2014oct_all humandb -buildver hg19

ADD REPLY • link 4.1 years ago by Kevin Blighe 88k

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Hi Kevin, I downloaded the database like this only. I can see the file in the humandb folder.

ADD REPLY • link 4.1 years ago by Dhara Awasthi ▴ 40

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Does it work with another 1000g version?; you are definitely running this from the correct directory?; you definitely have read access to the DB file?; does the command work on the supplied test data that comes with ANNOVAR (and not specifying -vcfinput)?

ADD REPLY • link 4.1 years ago by Kevin Blighe 88k

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