Explore rearrangements and copy-number amplifications in a cancer genome NOTE: SplitThreader will be going away soon. Please see the [README](https://github.com/MariaNattestad/SplitThreader) for more information.

Run SplitThreader

Variant calls

Copy number profile




Upload variant calls and a copy number profile

  1. Run Sniffles (for PacBio data) or Lumpy (for Illumina data, select output as bedpe format) and upload the .bedpe file. VCF files are supported, but do not always include the necessary information such as strand and number of reads, so some information may be missing. The script parses your file based on the format of VCF files from Manta, Delly, and Lumpy, and in some cases has to guess the strands from the variant types and other flags specific to each variant-caller's output. (example bedpe file , example csv file, example vcf file from Lumpy)
  2. Run Copycat on your bam file to convert to binned copy numbers, and upload the resulting .csv file (example)

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