Genome VCF | Sequencing.com

Genome VCF

Quickly create genome VCF (gVCF) files.

This easy-to-use app generates a gVCF file from a BAM file.

gVCF eliminates the ambiguity found with standard VCF by including data for all sites within a genome.

  • gVCF clearly differentiates variant, reference and no-calls for every site in the genome
  • Unlike standard VCF, a gVCF includes a call for a site even if the call is the same as the reference genome

 

This app creates gVCF files that conform to VCF v4.1 specifications.

  • The gVCFs produced by this app can be used by most tools that are compatible with VCF v4.1, such as IGV and Tabix.
  • To generate gVCF files compatible with VCF v4.2, please use the EvE Free or EvE Premium apps.

Free!

Log in to your Sequencing.com account and click the 'Add to My Apps' button located under the app icon. This app will instantly be added to your account and a 'Start App' button will appear under the app icon.

  1. Start the app by clicking the 'Start App' button
    • You can also start the app directly from My Apps
  2. Select a BAM file
    • If your file isn't in BAM format you can convert many formats into BAM using the EvE app.
  3. Select the reference genome that was used to generate the BAM file or select 'Auto Detect' and we'll automatically determine the reference genome
  4. Click 'Submit'. 
    • For advanced users: Before clicking Submit, first click 'Modify parameters' to view all modifiable parameters. You can define as many of these parameters as needed.
      • Before clicking Submit you can select to save your modified parameters. If saved, the next time you use this app all parameters will automatically be adjusted to your previously saved parameters.
        • Saves you time because you don't have to define parameters each time you use the app.

 

Once the app finishes you'll receive an email with a link to the results. You can also access results at any time by clicking Apps in the header and then clicking the Results tab.

  • The gVCF file generated by this app will be securely stored in your account.
    • You can download the file, share it with others and use it with your other apps.
  • This app utilizes code from gvctools' code repository. Code was last synced from the repo on Feb 5, 2016.
  • gVCF files produced by this app are written to VCF v4.1 specifications.
  • To create gVCF files compatible with VCF v4.2, please use the EvE Free or EvE Premium apps.

What's the difference between standard VCF and gVCF?

Standard VCF files include data for a specific chromosomal coordinate if the variant (alt) allele is detected. Ambiguity arises, however, when a chromosomal coordinate is not included in a VCF because this could mean either the reference allele was detected or there was a no call at that coordinate. This ambiguity is not acceptable when differentiating between a reference allele and a no-call can have a significant impact upon the interpretation of the data.

Chris Saunders: gvcftools