A variant caller for the GBA gene using WGS data

Related tags

MiscellaneousGauchian
Overview

Gauchian: WGS-based GBA variant caller

Gauchian is a targeted variant caller for the GBA gene based on a whole-genome sequencing (WGS) BAM file. Gauchian uses a novel method to solve the problems caused by the high sequence similarity with the pseudogene paralog GBAP1 and is able to detect variants accurately in the Exons 9-11 homology region, such as large deletions or duplications between GBA and GBAP1, and GBAP1-like variants in GBA, including p.A495P, p.L483P, p.D448H, c.1263del, RecNciI, RecTL and c.1263del+RecTL. In addition to these challenging variants, Gauchian also calls known pathogenic or likely pathogenic GBA variants classified in ClinVar. Please refer to our preprint for more details about the method.

Running the program

This Python3 program can be run as follows:

python -m gauchian --manifest MANIFEST_FILE \
                   --genome [19/37/38] \
                   --prefix OUTPUT_FILE_PREFIX \
                   --outDir OUTPUT_DIRECTORY \
                   --threads NUMBER_THREADS

The manifest is a text file in which each line should list the absolute path to an input BAM/CRAM file. For CRAM input, it’s suggested to provide the path to the reference fasta file with --reference in the command.

Interpreting the output

The program produces a .tsv file in the directory specified by --outDir. The fields are explained below:

Fields in tsv Explanation
Sample Sample name
is_biallelic_GBAP1-like_variant_exon9-11 Whether the sample is called as biallelic for GBAP1-like variants in exon9-11
is_carrier_GBAP1-like_variant_exon9-11 Whether the sample is called as a carrier for GBAP1-like variants in exon9-11
total_CN Total copy number of GBA+GBAP1
deletion_breakpoint_in_GBA_gene Whether the deletion breakpoint is in GBA gene if a deletion exists
GBAP1-like_variant_exon9-11 GBAP1-like variants called in exon9-11, two alleles separated by /
other_variants Other variants called (non-GBAP1-like variants or variants outside of exon9-11)

A .json file is also produced that contains more information about each sample.

Fields in json Explanation
Coverage_MAD Median absolute deviation of depth, measure of sample quality
Median_depth Sample median depth
deletion_CN CN of the unique region between GBA and GBAP1. This value plus 2 is the total CN
deletion_CN_raw Raw normalized depth of the unique region between GBA and GBAP1
variant_raw_count Supporting reads for each variant
snp_call GBA copy number call at GBA/GBAP1 differentiating sites
snp_raw Raw GBA copy number at GBA/GBAP1 differentiating sites
haplotypes Summary of haplotypes assembled across GBA/GBAP1 differentiating sites in Exon9-11
You might also like...
Data Structures and Algorithms Python - Practice data structures and algorithms in python with few small projects

Data Structures and Algorithms All the essential resources and template code nee

Adansons Base is a data management tool that organizes metadata of unstructured data and creates and organizes datasets.

Adansons Base is a data management tool that organizes metadata of unstructured data and creates and organizes datasets. It makes dataset creation more effective and helps find essential insights from training results and improves AI performance.

Open-source data observability for modern data teams
Open-source data observability for modern data teams

Use cases Monitor your data warehouse in minutes: Data anomalies monitoring as dbt tests Data lineage made simple, reliable, and automated dbt operati

A demo of a data science project using Kedro

iris Overview This is your new Kedro project, which was generated using Kedro 0.17.4. Take a look at the Kedro documentation to get started. Rules and

Data Poisoning based on Adversarial Attacks using Non-Robust Features

Data Poisoning based on Adversarial Attacks using Non-Robust Features Usage python main.py [-h] [--gpu | -g GPU] [--eps |-e EPSILON] [--pert | -p PER

Cisco IOS-XE Operations Program. Shows operational data using restconf and yang
Cisco IOS-XE Operations Program. Shows operational data using restconf and yang

XE-Ops View operational and config data from devices running Cisco IOS-XE software. NoteS The build folder is the latest build. All other files are fo

Run python scripts and pass data between multiple python and node processes using this npm module

Run python scripts and pass data between multiple python and node processes using this npm module. process-communication has a event based architecture for interacting with python data and errors inside nodejs.

ARRU seismic backprojection - Earthquake waveform detection and P/S arrivals picking on continuous data using ARRU phase picker Download and process GOES-16 and GOES-17 data from NOAA's archive on AWS using Python.
Download and process GOES-16 and GOES-17 data from NOAA's archive on AWS using Python.

Download and display GOES-East and GOES-West data GOES-East and GOES-West satellite data are made available on Amazon Web Services through NOAA's Big

Comments
  • UserWarning: multiple_iterators not implemented for CRAM

    UserWarning: multiple_iterators not implemented for CRAM

    When running with .cram file, got the following warnings /gauchian/depth_calling/snp_count.py:131: UserWarning: multiple_iterators not implemented for CRAM ignore_orphan=False /gauchian/depth_calling/haplotype.py:189: UserWarning: multiple_iterators not implemented for CRAM min_base_quality=13

    Will these warnings affect the quality of calls?

    opened by LNGDingj 1
Releases(v1.0.2)
Owner
Illumina
Illumina Open Source Software
Illumina
It is Keqin Wang first project in CMU, trying to use DRL(PPO) to control a 5-dof manipulator to draw line in space.

5dof-robot-writing this project aim to use PPO control a 5 dof manipulator to draw lines in 3d space. Introduction to the files the pybullet environme

Keqin Wang 4 Aug 22, 2022
Python Commodore BBS multi-client

python-cbm-bbs-petscii Python Commodore BBS multi-client This is intended for commodore 64, c128 and most commodore compatible machines (as the new Co

7 Sep 16, 2022
Capture screen and download off Roku based devices

rokuview Capture screen and download off Roku based devices Tested on Hisense TV with Roku OS built-in No guarantee this will work with all Roku model

3 May 27, 2021
Test for using pyIIIFpres for rara magnetica project

raramagnetica_pyIIIFpres Test for using pyIIIFpres for rara magnetica project. This test show how to use pyIIIFpres for creating mannifest compliant t

Giacomo Marchioro 1 Dec 03, 2021
All exercises done during the Python 3 course in the Video Course (World 1, 2 and 3)

Python3-cursoemvideo-exercises - All exercises done during the Python 3 course in the Video Course (World 1, 2 and 3)

Renan Barbosa 3 Jan 17, 2022
Streamlit — The fastest way to build data apps in Python

Welcome to Streamlit 👋 The fastest way to build and share data apps. Streamlit lets you turn data scripts into sharable web apps in minutes, not week

Streamlit 22k Jan 06, 2023
Tucan Discord Token Generator - Remastered

TucanGEN-SRC Tucan Discord Token Generator - Remastered Tucan source made better by me. -- idk if it works anymore Includes: hCaptcha Bypass Automatic

Vast 8 Nov 04, 2022
ThinkPHP全日志扫描工具,命令行版和BurpSuite插件版

ThinkPHP3和5日志扫描工具,提供命令行版和BurpSuite插件版,尽可能全的发掘网站日志信息 命令行版 安装 git clone https://github.com/r3change/TPLogScan.git cd TPLogScan/ pip install -r requireme

119 Dec 27, 2022
List of resources for learning Category Theory

A curated list of resources for studying category theory. As resources aimed at mathematicians are abundant, this list is aimed at materials whose target audience is not people with a graduate-level

Bruno Gavranović 100 Jan 01, 2023
Multiple GNOME terminals in one window

Terminator by Chris Jones [email protected] and others. Description Terminator was

GNOME Terminator 1.5k Jan 01, 2023
Integration between the awesome window manager and the firefox web browser.

Integration between the awesome window manager and the firefox web browser.

contribuewwt 3 Feb 02, 2022
Run CodeServer on Google Colab using Inlets in less than 60 secs using your own domain.

Inlets Colab Run CodeServer on Colab using Inlets in less than 60 secs using your own domain. Features Optimized for Inlets/InletsPro Use your own Cus

2 Dec 30, 2021
DRF magic links

drf-magic-links Installation pip install drf-magic-links Add URL patterns # urls.py

Dmitry Kalinin 1 Nov 07, 2021
navigation_commander is a ROS package to command the robot to navigate autonomously to each table for food delivery inside a hotel.

navigation_commander navigation_commander is a ROS package to command the robot to navigate autonomously to each table for food delivery inside a hote

ALEENA LENTIN 9 Nov 08, 2021
Web-based Sudoku solver built using Python. A demonstration of how backtracking works.

Sudoku Solver A web-based Sudoku solver built using Python and Python only The motivation is to demonstrate how Backtracking algorithm works. Some of

Jerry Ng 2 Dec 31, 2022
FindUncommonShares.py is a Python equivalent of PowerView's Invoke-ShareFinder.ps1 allowing to quickly find uncommon shares in vast Windows Domains.

FindUncommonShares The script FindUncommonShares.py is a Python equivalent of PowerView's Invoke-ShareFinder.ps1 allowing to quickly find uncommon sha

Podalirius 184 Jan 03, 2023
A project to explore and provide useful code for Mango Markets

🥭 Mango Explorer A project to explore and provide useful code for Mango Markets

Blockworks Foundation 160 Dec 19, 2022
The semi-complete teardown of Cosmo's Cosmic Adventure.

The semi-complete teardown of Cosmo's Cosmic Adventure.

Scott Smitelli 10 Dec 02, 2022
Notebooks for computing approximations to the prime counting function using Riemann's formula.

Notebooks for computing approximations to the prime counting function using Riemann's formula.

Tom White 2 Aug 02, 2022
Predict if a fuse is usable on an appliance depending on the fuse rating

fuse-feasibility-analysis Predict if a fuse is usable on an appliance depending on the fuse rating , Power rating and resistance in the appliance

Sebastian Muchui 4 Jul 21, 2022