gwas compression analysis

Run tabix experiments (snakemake)

stabix_mamba.yml

mamba create -n stabix -f stabix_mamba.yml
mamba activate stabix
snakemake -s scripts/bash/tabix_time.smk

or

mamba create -n stabix -f stabix_mamba.yml
mamba activate stabix
sbatch run_tabix_snakemake.sh

Run STABIX experiments (snakemake)

mamba create -n stabix -f stabix_mamba.yml
mamba activate stabix
snakemake -s scripts/bash/stabix_time.smk

or

mamba create -n stabix -f stabix_mamba.yml
mamba activate stabix
sbatch run_stabix_snakemake.sh

Plot main hexagonal heatmap

python scripts/python/plotting_scripts/publish.py \
 --data /path/to/data/ \
 --bed data/bed_files/hg19.protein_coding.bed \
 --out figures/

Details

file sizes	num blocks
p-value hits	sig SNPs

Plot combination results

python scripts/python/plotting_scripts/plot_compare.py \
 --root /path/to/data/ \
 --bed data/bed_files/hg19.protein_coding.bed \
 --out figures/

Details

Plot column results

python scripts/python/plotting_scripts/plot_columns.py \
 --decomp /path/to/data/ \
 --colors figures/colors.txt \
 --out figures/
   

Details