vcferr 1.0.2

Probabilistic VCF genotype error simulation

vcferr

The vcferr module is a lightweight error simulation framework. The tool operates on an input VCF and can probabilistically simulate the following error models for biallelic SNPs:

• rarr = Heterozygous drop out: (0,1) or (1,0) to (0,0)
• aara = Homozygous alt drop out: (1,1) to (0,1)
• rrra = Heterozygous drop in: (0,0) to (0,1)
• raaa = Homozygous alt drop in: (0,1) or (1,0) to (1,1)
• aarr = Double homozygous alt drop out: (1,1) to (0,0)
• rraa = Double homozygous alt drop in: (0,0) to (1,1)

In addition to error models, the tool includes functionality to inject probability of missingness:

• ramm = Heterozygous to missing: (0,1) or (1,0) to (.,.)
• rrmm = Homozygous ref to missing: (0,0) to (.,.)
• aamm = Homozygous alt to missing: (1,1) to (.,.)

Installation

The vcferr tool is delivered as a Python module.

To install from PyPi:

pip install vcferr

Alternatively, clone the vcferr GitHub repository and use pip from the root of the directory:

pip install .

Note that the following dependencies are used by vcferr:

• Python >=3.6.x
• pysam
• random
• click

Usage

The examples below demonstrate basic usage with the example.vcf.gz in the data/ directory of the vcferr GitHub repository.

The following is a basic example that simulates 20% heterozygous dropout:

vcferr data/example.vcf.gz --sample='sample1' --p_rarr=0.2

By default, vcferr will stream output of the VCF with errors simulated. However, if an argument is given for "output_vcf" then the VCF will be written to disk:

vcferr data/example.vcf.gz --sample='sample1' --output_vcf=data/sample1sim.example.vcf.gz --p_rarr=0.2

Note that multiple kinds of error can be simulated simulatenously:

vcferr data/example.vcf.gz --sample='sample1' --p_rarr=0.2 --p_raaa=0.1 --p_rrra=0.2 --p_aara=0

The tool can also simulate missingness:

vcferr data/example.vcf.gz --sample='sample1' --p_rarr=0.2 --p_raaa=0.1 --p_rrra=0.2 --p_aara=0 --p_rrmm=0.5