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bird-workflow's Introduction

bird-workflow

Repository to coordinate the effort to create a simplified workflow for running BIRD

bird-workflow's People

Contributors

tncowart avatar alexbarrera avatar brendan-kearney avatar

Watchers

avatar Tim Reddy avatar Keith Siklenka avatar avatar avatar Kuei-Yueh Ko avatar avatar avatar avatar Lee Edsall avatar avatar avatar avatar avatar

Forkers

brendan-kearney rairuhi

bird-workflow's Issues

Initial features request

Recap of the discussion points that originated this repository.

  • Extracting and tallying basecalls from mpileup
    - currently bash scripting and a python script from Alex
    - partition multiallelic sites
  • Consolidating mpileup data into an input file
    - currently python script from Alex
  • Options to threshold on DNA and/or RNA counts
  • Add a parallelization option that includes creation of the variable file
  • Option to include counts in the output file
  • Generation of QC plots
    - distribution of preg values
    - distribution of theta values

Important scripts and template code to follow

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