Variant Graph Comparison Tool

Kevin Jacobs <jacobs@bioinfomed.com>

vgraph is a command line application and Python library to compare genetic variants using variant graphs. Conventional methods used to compare variants apply heuristic normalization rules and then compare variants individually by matching based on genomic position and allele information. In contrast, vgraph utilizes a graph representation of genomic variants to precisely compare complex variants that are refractory to comparison using conventional methods.

Input

vgraph currently accepts block gzipped and indexed VCF and BCF files. Support for Complete Genomics var and masterVar formats will be added in a future version. vgraph also requires an indexed reference genome in FASTA+FAI format.

Output

vgraph outputs diagnostic only information to stdout. In repmatch mode, there are options to output either of the two input files with match status annotations. In dbmatch mode, the sample input file is output after copying all new INFO and FORMT annotations from the database file.

Usage

vgraph takes the following command line parameters:

usage: vgraph [-h] [--debug] [--profile] {repmatch,dbmatch} ...

positional arguments:
  {repmatch,dbmatch}  Commands
    repmatch          compare two replicate samples
    dbmatch           compare a database of alleles to a sample

optional arguments:
  -h, --help          show this help message and exit
  --debug             Output extremely verbose debugging information
  --profile           Profile code performance

The parameters for repmatch are:

usage: vgraph repmatch [-h] [--out1 OUT1] [--out2 OUT2] [--name1 N]
                       [--name2 N] --reference FASTA [-p N]
                       [--include-regions BED] [--exclude-regions BED]
                       [--include-file-regions BED]
                       [--exclude-file-regions BED] [--include-filter F]
                       [--exclude-filter F] [--min-gq N]
                       vcf1 vcf2

positional arguments:
  vcf1                  Sample 1 VCF/BCF input (- for stdin)
  vcf2                  Sample 2 VCF/BCF input (- for stdin)

optional arguments:
  -h, --help            show this help message and exit
  --out1 OUT1           Sample 1 VCF/BCF output (optional)
  --out2 OUT2           Sample 2 VCF/BCF output (optional)
  --name1 N             Name or index of sample in sample 1 file (default=0)
  --name2 N             Name or index of sample in sample 2 file (default=0)
  --reference FASTA     Reference FASTA+FAI (required)
  -p N, --reference-padding N
                        Pad variants by N bp when forming superloci
                        (default=2)
  --include-regions BED
                        BED file of regions to include in comparison
  --exclude-regions BED
                        BED file of regions to exclude from comparison
  --include-file-regions BED
                        BED file of regions to include for each input file
  --exclude-file-regions BED
                        BED file of regions to exclude from comparison for
                        each input file
  --include-filter F    Include records with filter status F. Option may be
                        specified multiple times or F can be comma delimited
  --exclude-filter F    Exclude records with filter status F. Option may be
                        specified multiple times or F can be comma delimited
  --min-gq N            Exclude records with genotype quality (GQ) < N

The parameters for dbmatch are:

usage: vgraph dbmatch [-h] [--name N] [-o OUTPUT] --reference FASTA [-p N]
                      [--include-regions BED] [--exclude-regions BED]
                      [--include-file-regions BED]
                      [--exclude-file-regions BED] [--include-filter F]
                      [--exclude-filter F] [--min-gq N]
                      database sample

positional arguments:
  database              Database of alleles VCF/BCF input (- for stdin)
  sample                Sample VCF/BCF input (- for stdin)

optional arguments:
  -h, --help            show this help message and exit
  --name N              Name or index of sample in sample file (default=0)
  -o OUTPUT, --output OUTPUT
                        Sample VCF/BCF output
  --reference FASTA     Reference FASTA+FAI (required)
  -p N, --reference-padding N
                        Pad variants by N bp when forming superloci
                        (default=2)
  --include-regions BED
                        BED file of regions to include in comparison
  --exclude-regions BED
                        BED file of regions to exclude from comparison
  --include-file-regions BED
                        BED file of regions to include for each input file
  --exclude-file-regions BED
                        BED file of regions to exclude from comparison for
                        each input file
  --include-filter F    Include records with filter status F. Option may be
                        specified multiple times or F can be comma delimited
  --exclude-filter F    Exclude records with filter status F. Option may be
                        specified multiple times or F can be comma delimited
  --min-gq N            Exclude records with genotype quality (GQ) < N

Installation

Before vgraph may be installed, your systems requires a C compiler, a functioning version of Python 3.5 or newer with development libraries installed, and the pip installer. The steps to install and ensuring these tools are functional depend on your operating system and personal configuration. Proceed only once these pre-requisites are available.

First install the latest version of the Cython and pysam packages:

pip install -U Cython
pip install -U pysam

If all these steps have succeeded, then install vgraph:

pip install -U git+https://github.com/bioinformed/vgraph.git