Guide

Introduction

snipar (single nucleotide imputation of parents) is a python library for imputing missing parental genotypes from observed genotypes in a nuclear family, and for performing family based genome-wide association and polygenic score analyses using the resulting imputed parental genotypes.

snipar contains command line scripts:

1. for inferring IBD segments shared between siblings (ibd.py)

2. imputing missing parental genotypes from observed parent/offspring genotypes and IBD segments (impute.py),

3. performing genome-wide estimation of direct genetic effects, non-transmitted coefficients, and population effects of SNPs (gwas.py),

4. for estimating direct effects and non-transmitted coefficients of polygenic scores (pgs.py),

5. and for estimating genome-wide correlations between direct and population effects and direct effects and non-transmtitted coefficients (correlate.py)