UrgentΒΆ

  1. How best to deal with multiple chrom namin schemes?
  2. How best to track and handle multiple genome versions.

3. effect ranking system so that group by can be for highest impact Ideas ===== 4. Popgen:

a. coefficient of inbreeding b.
  1. Visualization
    1. make plots of a given region/genes with snps on top, as well as the allele frequencies, etc.
    2. use genometools libraries.
    3. manhattan plots.
  2. Use Pytables for really big files, as the genotype table can be stored as fixed-width records.

  3. Interface

    pop load pop get

    # use a raw SQL query

    pop get -q “SELECT...”

    # use short cuts that automatically generate the appropriate queries behind the scenes. pop get -s variants pop get -s tstv pop get -s sfs –binsize 0.01 pop get -s samples pop get -s lof

    pop stats

    fst - model after vcftools?

comments powered by Disqus

This Page

Edit and improve this document!

This file can be edited directly through the Web. Anyone can update and fix errors in this document with few clicks -- no downloads needed.

  1. Go to Urgent on GitHub.
  2. Edit files using GitHub's text editor in your web browser (see the 'Edit' tab on the top right of the file)
  3. Fill in the Commit message text box at the bottom of the page describing why you made the changes. Press the Propose file change button next to it when done.
  4. Then click Send a pull request.
  5. Your changes are now queued for review under the project's Pull requests tab on GitHub!

For an introduction to the documentation format please see the reST primer.