I have been trying to run a benchmark test on one the haplotype phasing application. I tried to navigate around to find tutorials for it and found this to be a good one: https://portal.biohpc.swmed.edu/content/training/bioinformatics-nanocourses/gwas/zhan-phasing-workshop/
I like this tutorial because it is simple and straight forward. The haplotype database I am trying to use is from CEU (NA12891) which is considered a gold standard. I am able to find the NA12891 database in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ but still can't narrow down the same exact database.
These are the data I am looking for :
- hapmap3_r2_b36_chr20.haps (HAPS file)
- all.sample (SAMPLE file)
- hapmap3_r2_b36_chr20.legend (LEGEND file)
- genetic_map_chr20_combined_b36.txt (Genetic map file)