<h3 align="center">vcfgl</h3> <p align="center"> <a href="https://github.com/isinaltinkaya/vcfgl/releases/latest"><img src="https://img.shields.io/github/v/release/isinaltinkaya/vcfgl?labelColor=white&color=blue"/></a> <a href="https://github.com/isinaltinkaya/vcfgl/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-GPLv3.0-purple.svg?labelColor=white"/></a> <img alt="GitHub Actions Workflow Status" src="https://img.shields.io/github/actions/workflow/status/isinaltinkaya/vcfgl/test.yml?labelColor=white"> <a href="https://bio.tools/vcfgl"><img src="https://img.shields.io/badge/bio.tools-vcfgl-orange?labelColor=white"/></a> <a href="http://dx.doi.org/10.1093/bioinformatics/btaf098"><img src="https://img.shields.io/badge/Bioinformatics-10.1093%2Fbtaf098-black?labelColor=white&color=darkred"/></a>  </p> <p align="center"> Genotype likelihood simulator for VCF/BCF files <br />  <br /> <br /> <a href="https://github.com/isinaltinkaya/vcfgl">Installation</a> <b>·</b> <a href="https://github.com/isinaltinkaya/vcfgl/doc/tutorial.MD">Tutorial</a> <b>·</b> <a href="https://github.com/isinaltinkaya/vcfgl/issues/new?assignees=&labels=bug&projects=&template=report-a-bug.md&title=%5BBUG%5D">Report Bug</a> <b>·</b> <a href="https://github.com/isinaltinkaya/vcfgl/issues/new?assignees=&labels=enhancement&projects=&template=feature_request.md&title=%5BFR%5D">Request Feature</a> <b>·</b> <a href="#how-to-cite">Cite</a> </p> </div> <details open> <summary>Table of Contents</summary> <ol> <li> <a href="#overview">Overview</a> </li> <li> <a href="#installation">Installation</a> <ul>     </ul> </li> <li><a href="#usage">Usage</a>  </li> <li> <a href="#tutorials">Tutorials</a></li> <li><a href="#quickstart-for-mstoglf-users">Quickstart for msToGlf users</a></li> <li><a href="#contact">Contact</a></li> <li><a href="#how-to-cite">How to cite</a></li> </ol> </details>

Overview

vcfgl is a lightweight command-line program for simulating VCF/BCF and gVCF files. It allows you to simulate sequencing data with various parameters, such as read depth, base-calling error rates, quality score errors, and genotype likelihood models.

Installation

You can install vcfgl using one of the following methods:

→ Method 1: Using release tarball (recommended)

You can download the latest release tarball from the GitHub releases page.

→ Method 2: Using HTSlib submodule

This method uses the htslib submodule included in the repository.

git clone https://github.com/isinaltinkaya/vcfgl.git;
cd vcfgl;
make;

→ Method 3: Using systemwide HTSlib installation

This method assumes you have a systemwide htslib installation.

git clone https://github.com/isinaltinkaya/vcfgl.git;
cd vcfgl;
make HTSSRC="systemwide";

→ Method 4: Using specified HTSlib path

This method allows you to specify the path to your htslib installation.

git clone https://github.com/isinaltinkaya/vcfgl.git;
cd vcfgl;
make HTSSRC=path/to/htslib;

For detailed compilation instructions, in vcfgl directory, run:

<details><summary> <code> make help </code></summary> <pre>$ make help ---------------------------------------- Program: vcfgl Version: v0.4-bb8df2d License: GNU GPLv3.0 ---------------------------------------- Usage: make [target] [FLAG=value...] Targets: help - Print this help message dev - Compile in developer/debug mode (activates flags: -g -Wall -O0) clean - Clean up the directory test - Run unit tests Flags: HTSSRC - Specifies the source of HTSlib. Values: (empty) - Use the HTSlib submodule [default] systemwide - Use the systemwide HTSlib installation /path/to/htslib - Use the HTSlib installation at /path/to/htslib Examples: make - Compile in release mode using HTSlib submodule make HTSSRC=/path/to/htslib - Compile in release mode using /path/to/htslib make dev HTSSRC=systemwide - Compile in developer mode using the systemwide HTSlib installation Note: If no values are provided for HTSSRC, CXX, CXXFLAGS, or LIBS, defaults will be used. </pre> </details>

Usage

You can access the command-line help page using vcfgl --help or vcfgl -h:

<details open> <summary> <code> vcfgl --help </code></summary> <pre> <pre> Usage: vcfgl -i <input> [options] -h, --help _____________________ Print this help message and exit -v, --version __________________ Print version and build information and exit Option descriptions: -s, --long-option TYPE [X] _____ Description -s Short option (if any) --long-option Long option TYPE Type of the argument value, can be: - INT (integer) - INT+ (additive integer: sum values to use together - FLOAT (floating point number) - STRING (string) - FILE (filename) - x|y|z (one of the listed values x, y or z) [X] Default argument value (if any) _____ Connector to the option description for better readability General options: -V, --verbose INT [0] ___________ Verbosity level -@, --threads INT [1] ___________ Number of threads -s, --seed INT [time] ___________ Random seed for initializing the random number generator Input/Output: -i, --input FILE ________________ Input VCF/BCF file --source [0]|1 ______________ 0: Input REF/ALT alleles are in binary format (REF=0, ALT=1; typically outputted from msprime BinaryMutationModel) 1: Input REF/ALT alleles are in VCF format (REF=i, ALT=j(,k..); i, j and k from {A,C,G,T}; i.e. the regular VCF format) -o, --output STRING ['output'] __ Output filename prefix -O, --output-mode [b]|u|z|v _____ b: Compressed BCF (.bcf), u: uncompressed BCF (.bcf), z: compressed VCF (.vcf.gz), v: uncompressed VCF (.vcf) Simulation parameters: -d, --depth FLOAT|'inf' _________ Mean per-site read depth ('inf') Simulate true values (requires: -addFormatDP 0 -addInfoDP 0) -df, --depths-file FILE __________ File containing mean per-site read depth values for each sample. One value per line. -e, --error-rate FLOAT __________ Base-calling error probability -eq, --error-qs [0]|1|2 __________ 0: Do not simulate errors in quality scores. Assumes all quality score assignments are correct 1: Simulate site-specific errors in the probability of wrong base calls (requires: -bv FLOAT) 2: Simulate the errors in the reported quality scores and genotype likelihoods (requires: -bv FLOAT) -bv, --beta-variance FLOAT _______ Designated variance for the beta distribution -GL, --gl-model 1|[2] ____________ Genotype likelihood model to be used in simulation 1: Genotype likelihood model with correlated errors (a.k.a. Li model, samtools model, angsd -GL 1) 2: Canonical genotype likelihood model with independent errors (a.k.a. McKenna model, GATK model, angsd -GL 2) --gl1-theta FLOAT [0.83] ___ Theta parameter for the genotype likelihood model 1 (requires: -GL 1) --qs-bins FILE _____________ File containing the quality score binning to be used in the simulation --precise-gl [0]|1 _________ 0: Use the discrete phred-scaled error probabilities in the genotype likelihood calculation 1: Use precise error probabilities in the genotype likelihood calculation (requires: -GL 2) --i16-mapq INT [20] ________ Mapping quality score for I16 tag (requires: -addI16 1) --gvcf-dps INT(,INT..) _____ Minimum per-sample read depth range(s) for constructing gVCF blocks (requires: -doGVCF 1) Example: `--gvcf-dps 5,10,20` will group invariable sites into three types of gVCF blocks: [5,10), [10,20) and [20,inf) Sites with minimum depth < 5 will be printed as regular VCF records. --adjust-qs INT+ [0] _______ 0: Do not adjust quality scores 1: Use adjusted quality scores in genotype likelihoods (requires: --precise-gl 0) 2: Use adjusted quality scores in calc

Vcfgl

Install / Use

README