Calculating summary statistics on real data

Calculating summary statistics on real data

Data format

Real data must be in PLINK .tped file with 0's and 1's.
Sites in rows, individuals in columns (first 4 columns chr, rsnumber, site_begin, site_end). The populations must be in the same order as specified in the model file for the simulations.

Put the individuals in teh correct order
https://www.cog-genomics.org/plink2/data#indiv_sort

plink --bfile bfile --indiv-sort f sample_order.txt --make-bed --out bfile_ordered

To get in the .tped format from .bed .bim .fam with 0's and 1's refer to
https://www.cog-genomics.org/plink2/formats#tped

plink --bfile bfile --recode transpose 01 --output-missing-genotype N --out tfile01

Usage

real_data_ss.py takes 5 arguments:

1. model_file
2. param_file
3. output_dir
4. genome_file
5. array_file

e.g.

python real_data_ss.py examples/eg1/model_file_eg1.csv examples/eg1/param_file_eg1.txt out_dir ~/data/HapMap_example/test_10_YRI_CEU_CHB.tped ~/data/HapMap_example/test_10_YRI_CEU_CHB_KHV_hg18_ill_650.tped