Hello, am writing my own pipeline in python in order to annotate bacterial genome MTB, am new in this field and am a bit lost , I converted my vcf to appropriate annovar input format, then i got stack, i have to use dbSNP to annotate snp and hrv37 as the reference genome for annotation but dont really know the correct command format of what i really need to provide more. i read the manual but it s not really helping me. Any one with experience in using annovar to annotate bacterial genomes? Thanks in advance
The tool form itself for Annovar wrapped within Galaxy will guide where to enter these inputs. Galaxy can be used many ways: https://galaxyproject.org/choices/
There are two versions of the Galaxy Annovar wrapper that could be reviewed to see how the command is constructed for Galaxy. These are abstracted but may still be helpful. Search for "Annovar" here https://toolshed.g2.bx.psu.edu/ and follow the links to the development repositories. Or, log in to review the "tip" repository files. Click the repository name, then the tool name, and find this review option in the upper right corner menu.
Support for command-line tool usage is beyond the scope of this forum. A better choice would be to review prior Q&A at other general bioinformatics forums and to potentially ask a question if you need more clarification. A search like this will find resources for Annovar command-line usage. Some forum sites are listed in the top hits but also scroll down to the bottom of the search results page where there are related commonly searched terms that include "tutorial" and "example". Most of these are for line-command usage.
Thanks! Jen, Galaxy team