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tf2 / CNest

Copy Number Methods for Detection and Genome Wide Association Tests
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A working version of cnest.py for all steps #4

Closed smshuai closed 3 years ago

smshuai commented 3 years ago

This version of cnest.py has been tested on 1,000 WES for all steps.

Main new features:

  1. fast read counting with hts-nim-tools
  2. works with Nextflow for easy scaling-up to a large number of samples on HPC (SLURM/LSF/etc.) or cloud environments
  3. cov_file auto-generation
  4. From bin to rbin in one step (original steps 4-6 combined)
  5. mixed_ref_samples auto-filled to batch_size
  6. Both sample_name and sample_index are supported now