gene_summary and gene_detailed in Gemini

[a113n]

To be fully compatible with Gemini, is there any way for us to include the gene_summary and gene_detailed tables in the DB output as well?

One suggestion would be porting arq5x/gemini/gemini/gene_table.py to vcf2db, while allowing GTF file input from user.

Thanks a lot.

[brentp]

I had planned to deprecate those tables. Do you use them? If I know the use-case, maybe we can figure out a workaround.

[a113n]

My existing Gemini pipeline is based on GRCh37, and I want that to be
almost 100% compatible when I port to GRCh38. As part of the provenance
requirements of my environment, gemini's ability to bundle gene annotations
with variants is essential for me.

Therefore I have drafted a branch that allows me to include gene
annotations as well using vcf2db. The codes were tested against GRCh38
annotations only. The URL to my branch can be found below:
https://github.com/a113n/vcf2db/tree/gene_table?files=1

Hope that's useful for someone else who need that feature!

On Wed, 19 Oct 2016 at 8:29 PM, Brent Pedersen - Bioinformatics <
[email protected]> wrote:

I had planned to deprecate those tables. Do you use them? If I know the
use-case, maybe we can figure out a workaround.

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