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  • 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?

  • #2
    Yes, you can. IGV can read a lots of data formats.

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    • #3
      Originally posted by TiborNagy View Post
      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 ?

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      • #4
        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, 12:32 PM.

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        • #5
          I have worked with BED files, but IGV can read custom files:
          If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.

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          • #6
            Originally posted by TiborNagy View Post
            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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