Write script to get gene-aggregate counts for DB columns in annotated VCF

[eweitz]

Write a script to get gene-aggregated counts for DB columns in an annotated VCF.

Input:

• An annotated, filtered VCF file output from the script by @nicovbing that implements Issue 8

Output:

• Insert row in the "GeneUserData" table with counts for the number of variants in columns "In ClinVar", "High impact", "Missense", etc. -- one row per gene per upload
• Foreign key should be Entrez Gene ID (column named "slot", perhaps)

[CarlosBorroto]

We are now going with loading the VCF data into Solr.

This script needs to get integrated into our pipeline.

scripts/vcftools.py vcf-to-json --upload_hash 010101 path/to/annotated.vcf

We still need to write a script to get the data into Solr. @vlaufer maybe you want to take on that?

[ohjuarez]

All you need is to run this command:

/solr/SOLR_HOME/bin/post.sh

Octavio Juarez-Espinosa, PhD
Contractor –MSC, Inc. Scripting Developer
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, Room 4A72
Rockville, MD 20852
Mobile 2407628157
Office 12406692760

From: Carlos Borroto <notifications@github.commailto:notifications@github.com>
Reply-To: DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution <reply@reply.github.commailto:reply@reply.github.com>
Date: Wednesday, August 5, 2015 at 12:55 PM
To: DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution <NCBI_August_Hackathon_Push_Button_Genomics_Solution@noreply.github.commailto:NCBI_August_Hackathon_Push_Button_Genomics_Solution@noreply.github.com>
Subject: Re: [NCBI_August_Hackathon_Push_Button_Genomics_Solution] Write script to get gene-aggregate counts for DB columns in annotated VCF (#11)

We are now going with loading the VCF data into Solr.

This script needs to get integrated into our pipeline.

scripts/vcftools.py vcf-to-json path/to/annotated.vcf

We still need to write a script to get the data into Solr. @vlauferhttps://github.com/vlaufer maybe you want to take on that?

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Reply to this email directly or view it on GitHubhttps://github.com//issues/11#issuecomment-128069257.