Scott T Small

Dear Dr. Hickey, I am using Progressive Cactus to align mosquito genomes. Mosquito genomes are highly heterozygous with levels of divergence of >1% between chromosomes in the same individual. Most...

shiny app interface code

1

Hi @JimWhiting91, really liking this code base. Would you consider making the shiny app interface available as well? It would be really helpful for data exploration during collaboration. thanks, @stsmall

--pi not an option

3

Hi, I recently started using your code to estimate f2, since I couldnt seem to get AdmixTools to compile correctly. I have got most of the tests listed in the...

Out of bounds error during normalization: freebayes

7

Hi Brad, I reran the same files with 0.2.1 and received a different set of errors. It again halted during the processing/normalization of the freebayes joint calling file. If I...

What is a solution to the dangling nodes error?

1

Hi @awohns, I am getting an error stating that there are dangling nodes present when running tsdate. I attempted to simplify the tree before preprocessing and running tsdate, but that...

lmdb out of memory error on tutorial example

33

Hi, I keep getting an out of memory error even when running the toy example in the tutorial (under the msprime simulate). I can run the simulation step and produce...