Skip to main content
Join the official 2020 Python Developers SurveyStart the survey!

No project description provided

Project description

# BABACHI: Backgroud Allelic Dosage Bayesian Checkpoint Identification [![DOI](https://zenodo.org/badge/255952669.svg)](https://zenodo.org/badge/latestdoi/255952669) <br> BABACHI is a tool for Background Allelic Dosage (BAD) genomic regions calling from non-phased heterozygous SNVs. It is aimed at estimation of BAD on low-coverage sequencing data, where the precise estimation of allelic copy numbers is not possible.

BAD corresponds to the ratio of Major copy number to Minor copy number.

BABACHI takes in a vcf-like .tsv file with heterozygous SNVs sorted by genome positions (ascending). The input file must contain the following first 7 columns: chromosome, position, ID, reference base, alternative base, reference read count, alternative read count All lines, starting with # are ignored.

The output is a .bed file with BAD annotations.

## Installation

` pip3 install babachi `

## Requirements ` python >= 3.6 `

## Usage ` babachi <options>... ` To get full usage description one can execute: ` babachi --help `

## Quick start To perform a test run: ` babachi --test `

The BABACHI tool is maintained by Sergey Abramov and Alexandr Boytsov.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for babachi, version 1.4.0
Filename, size File type Python version Upload date Hashes
Filename, size babachi-1.4.0-py3-none-any.whl (368.1 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size babachi-1.4.0.tar.gz (13.4 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page