search

zjnolen / PopGLen

Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.
https://zjnolen.github.io/PopGLen/
GNU General Public License v3.0
5 stars 0 forks source link

Make pruning optional for NGSrelate and enable allele frequency based coefficients #49

Closed zjnolen closed 2 weeks ago

zjnolen commented 1 month ago

Allow user to decide if pruning is desired for NGSrelate, but keep it on by default as it assumes independence.

Right now, the allele frequency based metrics don't work because we don't provide allele frequencies. Add an option to do this. Doing this also makes an easy way to expose the allele frequency outputs as requestable outputs instead of by products of other analyses as they are now.

zjnolen commented 1 month ago

Pruning now optional, allele frequency metrics will take a bit more time and will be in the next version.