This project describes an automated pipeline to calculate the relatevie burden risk between two populations.
Python (recommended version >= 3.7)
An example is prepared in the project Example folder, executable as
cd /path/to/brrAB/Example
sh run_example.sh
Group Sample
populationA sample1
populationA sample2
populationB sample3
populationB sample4
outgroupC sample5
Brr can be easily run from anno vcf using snpEff:
python ../brrAB.py -f in.anno.vcf.gz -A populationA -B populationB -C outgroupC -w work_dir -G group_infos.tsv
(Optional) if you got genotype frequence file (gt_freq_info.tsv), and want to rerun burden risk,use:
python ../brrAB.py -f gt_freq_info.tsv -A populationA -B populationB -C outgroupC -w work_dir -G group_infos.tsv
(Optional) To specify a particular frequence (e.g. to filter the >= 0.6 in population), use:
--freq 0.6
(Optional) To specify a fix sites for jackknifes (default is 1/5 of total sites), use:
--fix_sites 100000