UrgentΒΆ
- How best to deal with multiple chrom namin schemes?
- 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.
- Visualization
- make plots of a given region/genes with snps on top, as well as the allele frequencies, etc.
- use genometools libraries.
- manhattan plots.
Use Pytables for really big files, as the genotype table can be stored as fixed-width records.
- 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?