Variant Discovery

Halotype-based variant caller for sequencing data including next-generation sequencing (NGS).

This app combines powerful cloud computing with the Platypus tool for variant detection/discovery. It analyzes a BAM file and generates a VCF file that contains a list of identified variants including genotype calls and likelihoods. 

Use this app to detect the following types of variants in BAM files from whole genome sequencing (WGS) and exome sequencing: 

  • SNPs
  • multinucleotide variants (also known as MNPs)
  • deletions and insertions (DIPs) that are less than one read length


Compatibility Information

This app is only compatible with BAM files obtained from genome sequencing. When this app is started, only BAM files (filenames that end with .bam) will be able to be selected.

$19 = unlimited use for 30 days

  1. Start the app
  2. Select a BAM file
    • You can select any BAM file in your account. This includes files you've uploaded, files generated by one or your apps and files that have been shared with you by others.
  3. Select the BAM file's reference genome.
    • Alternatively, you can choose 'Auto-detect' and your file's reference genome will be automatically determined.
  4. Click submit


You'll receive an email notification with a link to the app results, which will be a downloadable VCF file. The VCF file will be stored in your account and you can also use it with other apps.

  • Platypus tool. Wellcome Trust Centre for Human Genetics
  • Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R. F. Twigg, WGS500 Consortium, Andrew O. M. Wilkie, Gil McVean, Gerton Lunter.  Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nature Genetics (2014) doi:10.1038/ng.3036