Visualize variants annotated with ANNOVAR

Nilaksha · 03-25-2014, 12:17 AM

Hey all,

I'm developing a pipeline for NGS data analysis. I'm pretty much ok with the steps up to variant calling (I'm using GATK for that) and then I use the already built VCF file to convert it to an ANNOVAR compatible file for annotation. My problem is that, how can I incorporate ANNOVAR annotated files (there are several files I have got using Gene based/Filter based and Region based annotation) along with the VCF file in analysis. Can I add ANNOVAR annotated files as separate tracks along with VCF in visualisation programs like IGV?

TiborNagy · 03-25-2014, 07:08 AM

Yes, you can. IGV can read a lots of data formats.

Nilaksha · 04-06-2014, 10:56 PM

Quote:

Originally Posted by TiborNagy

Yes, you can. IGV can read a lots of data formats.

I tried importing csv file obtained by table_annovar.pl script of ANNOVAR to IGV but had no luck. Is there any particular method that worked for you ?

blakeoft · 04-07-2014, 01:28 PM

I'd like to know this too. I've tried opening file.exonic_variant_function and file.variant_function, and neither are visualized by IGV. The best thing I can think of is to add the appropriate headers to the Annovar output to make it look like a vcf. I guess some fields will have to be added as well.

EDIT: I just looked at the Annovar output again and it looks like it's going to need a lot more work than simply adding a header and some fields. But I think it might still be doable. I'll post a solution if I come up with one.

TiborNagy · 04-08-2014, 04:41 AM

I have worked with BED files, but IGV can read custom files:
https://www.broadinstitute.org/igv/custom_file_formats

Nilaksha · 04-08-2014, 08:44 PM

Quote:

Originally Posted by TiborNagy

I have worked with BED files, but IGV can read custom files:
https://www.broadinstitute.org/igv/custom_file_formats

Hey thanks a lot,

I guess I can work it out now/

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03-25-2014, 12:17 AM	#1
Nilaksha Member Location: Sri Lanka Join Date: Mar 2014 Posts: 19	Visualize variants annotated with ANNOVAR Hey all, I'm developing a pipeline for NGS data analysis. I'm pretty much ok with the steps up to variant calling (I'm using GATK for that) and then I use the already built VCF file to convert it to an ANNOVAR compatible file for annotation. My problem is that, how can I incorporate ANNOVAR annotated files (there are several files I have got using Gene based/Filter based and Region based annotation) along with the VCF file in analysis. Can I add ANNOVAR annotated files as separate tracks along with VCF in visualisation programs like IGV?

04-07-2014, 01:28 PM	#4
blakeoft Member Location: Connecticut Join Date: Oct 2013 Posts: 79	I'd like to know this too. I've tried opening file.exonic_variant_function and file.variant_function, and neither are visualized by IGV. The best thing I can think of is to add the appropriate headers to the Annovar output to make it look like a vcf. I guess some fields will have to be added as well. EDIT: I just looked at the Annovar output again and it looks like it's going to need a lot more work than simply adding a header and some fields. But I think it might still be doable. I'll post a solution if I come up with one. Last edited by blakeoft; 04-07-2014 at 01:32 PM.

03-25-2014, 07:08 AM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	Yes, you can. IGV can read a lots of data formats.

04-08-2014, 04:41 AM	#5
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	I have worked with BED files, but IGV can read custom files: https://www.broadinstitute.org/igv/custom_file_formats