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# BABACHI: Backgroud Allelic Dosage Bayesian Checkpoint Identification BABACHI is a tool for constant Background Allelic Dosage (BAD) genome regions calling from non-phased heterozygous SNPs. 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 SNPs 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.
` 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.
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