Question about opensource SNP tools from a Sysadmin

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6.0 years ago

aravindh • 0

Hello.

I'm a sysadmin with no knowledge of bioinformatics tools.

At my work, researchers are using a tool - BC SNP to store SNP data and perform analysis on it.

Are there any open source tools that we can use to replace it?

Thanks in advance for any suggestions.

snp genome • 1.0k views

ADD COMMENT • link 6.0 years ago by aravindh • 0

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Never heard about it, is it from this company?

http://www.bcplatforms.com

ADD REPLY • link 6.0 years ago by h.mon 35k

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and perform analysis on it.

You'll have to be a bit more specific here.

ADD REPLY • link 6.0 years ago by WouterDeCoster 47k

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For storing SNPs you can consider platforms like Gemini (https://gemini.readthedocs.io/en/latest/) and LOVD (http://www.lovd.nl/3.0/home). But I am not sure if they are compatible with commercial software output/export formats.

Since you are a sysadmin (assuming that you can handle db as well), you can create db (tables) using HL-7 (now FHIR) recommended clinical genomics database schema. FHIR (HL-7) clinical genomics furnishes UML (db schemal) as well, if i understand correct. They support versioning as well.

ADD REPLY • link 6.0 years ago by cpad0112 21k

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