Question: How can I add OMIM and HGMD data file on action right away to my VCF file?
3
gravatar for Bahar
3.4 years ago by
Bahar40
Iran
Bahar40 wrote:

I'm currently designing a workflow to analyze some exome sequencing data (VCF).

Now, I'd like to add OMIM data and HGMD data to my VCF file.

but I couldn't download some database that include them or  find any software to annotate this data online or offline. 

Do you know where I could find this kind of data file or which software doing those ?

Regards.

Bahar 

 

vcf omim hgmd annotation exome • 2.8k views
ADD COMMENTlink modified 4 months ago by zx87547.1k • written 3.4 years ago by Bahar40
2
gravatar for alons
3.4 years ago by
alons270
Rehovot
alons270 wrote:

Hi Bahar, 

We use the recommended tool SnpEff for variant annotation in VCFs, mainly to predict AA changes and effects. We also annotate the ID field with DbSNP using SnpSift (under the same project). However, to my knowledge there's also an option to annotate the VCF with several other clinical databases such as OMIM, check this link:
http://snpeff.sourceforge.net/protocol.html

SnpEff:
http://snpeff.sourceforge.net/

Hope this helps,
Alon

ADD COMMENTlink written 3.4 years ago by alons270
1

It`s great! Thank you so much Dear Alon, I will try it :)

ADD REPLYlink written 3.4 years ago by Bahar40
1

Great! Glad to hear it dear Bahar, I hope it will help you! :)

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by alons270
1

Another tool that you may find complementary (and which takes snpEff or VEP annotated VCFs as input, and performs additional annotations) is GEMINI. It also transforms the VCF data into a SQLite3 formated database and can contain pedigree information. It has a diverse set of tools to analyze exomes as trios, or select variants that fit specific inheritance patterns, genotype constraints, etc.

ADD REPLYlink written 3.4 years ago by Dan Gaston7.1k

oh yes, GEMINI is great. Do you know GIMINI can add publications PMID or the other sours of publications?

ADD REPLYlink written 3.4 years ago by Bahar40
1

It doesn't add any PMIDs. It does all of its annotations based on downloaded BED and VCF files and not any live queries to the web. 

ADD REPLYlink written 3.4 years ago by Dan Gaston7.1k

Thank you so much for your kind guidance.

ADD REPLYlink written 3.4 years ago by Bahar40
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