How to use ANNOVAR with bacterial genome?

Question: How to use ANNOVAR with bacterial genome?

15 months ago by

yarmda • 0

yarmda • 0 wrote:

I am trying to automatically generate annotations for a VCF file generated from the Mtb H37Rv genome. ANNOVAR seems like a possible route to do this, but each of its scripts require a --buildver parameter which indicates the version of the genome in use.

I have my VCF file and a file of Mtb genome annotations in GFF3 format, but it appears that I need some database, as well. Can anyone clarify this? The ANNOVAR documentation all make reference to the human genome.

variant annotation annovar • 557 views

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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by yarmda • 0

15 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool is natively indexed for hg19 plus two other genomes (neither are yours).

Try creating a custom genome of the target genome. This creates a "database" that you can assign to inputs which is then interpreted by the tool. I haven't tested using a CG with data and this tool recently, so please let us know if that does not solve the immediate issue (after confirming input formatting, etc).

Help:

https://galaxyproject.org/learn/custom-genomes/
http://annovar.openbioinformatics.org/en/latest/ (see "inputs" if you need help with expected input formatting when these are sourced from datasets in the history)

Please be aware the version 0.2 of the tool wrapper in Galaxy has a known issue. Using version 0.1 is recommended for now. Ticket for tracking progress on the fix: https://github.com/galaxyproject/galaxy/issues/4001

Thanks! Jen, Galaxy team

ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

When you say it creates a "database" what exactly do you mean? I started following the steps to produce a custom genome - I uploaded my ref genome and used the normalize fasta tool, but this just produces a slightly differently formatted fasta file. This may work, but then what do I include as the "buildver" parameter? Do I need to specify a protocol parameter, too? What would that be for a custom database buildver?

Thanks, Dave

ADD REPLY • link written 15 months ago by yarmda • 0

Create a Custom Build from the normalized custom genome fasta file. Instructions are in the first link above.

All of your custom builds will be listed along with the natively indexed builds under the Edit Attributes "database/build" menu and can be assigned to datasets. How-to: https://galaxyproject.org/support/datatypes-and-tools/

ADD REPLY • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

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