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?

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