ryhui/imputation-pipeline

imputation-pipeline

This repository contains scripts used in an imputation pipeline for low-coverage (0.05-1x) ancient genomes.

imputation_pipeline.snakefile

Default pipeline, including down-sampling, genotype likelihood calling in ATLAS, and imputation in Beagle. It is written as a snakemake workflow, but bash commands can be easily extracted from the "shell" sections.

local_imputation_pipeline.sh

(Author: Eugenia D'Atanasio)

Pipeline used for local imputation when only genotypes at certain positions are of interest.

pmd_filter.py

Filters out GLs that could result from deamination (C -> T changes).

compare_accuracy.py

Compares imputed and true genotypes to produce the accuracy table for various allele frequency bins.