This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Annovar coding_change error

Hi I'm trying to use Annovar coding_change program but I keep getting syntax error, any idea why?

perl coding_change.pl S01.exonic_variant_function humandb/hg19_refGene.txt humandb/hg19_refGeneMrna.fa humandb/hg19_MT_ensGene.txt humandb/hg19_MT_ensGeneMrna.fa -out S01
Syntax error
annovar coding_change
• 1,552 views • link
updated by Kevin Blighe Kevin Blighe • written by er.doug.ragnar • er.doug.ragnar

1 answer

You're supplying too many parameters. You cannot have both of the following pairs of parameters:

  • humandb/hg19_refGene.txt && humandb/hg19_refGeneMrna.fa
  • humandb/hg19_MT_ensGene.txt && humandb/hg19_MT_ensGeneMrna.fa

You can only supply 1 pair of these per go.

Kevin

• 1 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this