A toolkit to analyze genome variation data, built on top of the Genome Analysis Toolkit (GATK) with Clojure. It supports scoring for the Archon Genomics X PRIZE competition and is also a general framework for variant file comparison. It enables validation of variants and exploration of algorithm differences between calling methods by automating the process involved with comparing two sets of variants. For users, this integrates with the bcbio-nextgen framework to automate variant calling and validation. For developers, bcbio.variation provides command line tools and an API to clean and normalize variant data in VCF format avoiding comparison artifacts associated with different variant representations.
- Description of the comparison framework and variant calling algorithm comparisons
- Presentation from Bioinformatics Open Source Conference 2012
- Presentation overview of the project
- Howto description of interfacing with GATK
- Code documentation
The latest release is 0.2.3 (1 February 2015): bcbio.variation-0.2.3-standalone.jar. Run from the command line:
$ java -jar bcbio.variation-VERSION-standalone.jar [arguments]
The jar contains a full GATK commandline with additional walkers, as well as custom command line programs. The usage section below contains examples of using the library for variant comparison, normalization and ensemble calling. Note that bcbio.variation requires Java 1.7 since the underlying GATK libraries are not compatible with earlier versions.
As a library
To use as a library from Leiningen or Maven, follow the instructions on the clojars page.
The latest version is available directly from GitHub and requires Java 1.6 or better and Leiningen (version 2). Lein will automatically pull in all required dependencies.
Generate summary of concordance between variant calls
To compare two GATK compatible VCF files in a specific region:
$ java bcbio.variation.jar variant-utils comparetwo eval.vcf refcall.vcf ref.fa regions.bed
You can also tune many parameters with a YAML configuration file specifies the variant files for comparison. The project contains example configuration and associated variant files that demonstrate the features of the library and the configuration below has a description of available options.
$ java bcbio.variation.jar variant-compare config/reference-grading.yaml
$ java bcbio.variation.jar variant-compare config/method-comparison.yaml
Normalize a variant file
A tricky part of variant comparisons is that VCF format is flexible enough to allow multiple representations. As a result two files may contain the same variants, but one might have it present in a multi-nucleotide polymorphism while another represents it as an individual variant.
To produce a stable, decomposed variant file for comparison run:
$ java bcbio.variation.jar variant-prep your_variants.vcf your_reference.fasta
This will also handle re-ordering variants to match the reference file ordering,
essential for feeding into tools like GATK, and remapping hg19 to GRCh37
chromosome names. To additionally filter outputs by indel size, pass an argument
specifying the maximum indel size to include:
--max-indel 30. To retain
0/0) and no calls in the prepped file, use
Ensemble variant calls
bcbio.variation contains approaches to merge variant calls from multiple approaches. It normalizes all input VCFs, prepares a combined variant file with variants from all approaches, and then filter the combined file to produce a final set of calls.
To combine multiple variant calls into a single combined ensemble callset:
$ java bcbio.variation.jar variant-ensemble params.yaml reference.fa out.vcf in1.vcf in2.vcf in3.vcf
params.yaml-- parameters to us in preparing the ensemble set. See the example config for options.
reference.fa-- The reference FASTA file.
out.vcf-- Name of the final combined dataset.
in1.vcf... -- The input variant callsets to combine.
The o8 visualization framework provides a web interface to this toolkit, providing interaction with Galaxy and GenomeSpace, visualization of biological metrics associated with variants, reactive filtering and automated scoring.
Run GATK walker for variant statistics
$ lein uberjar $ java -jar target/bcbio.variation-RELEASE-standalone.jar -T VcfSimpleStatsWalker -R test/data/GRCh37.fa --variant test/data/gatk-calls.vcf --out test.png
Run custom GATK annotator
$ lein uberjar $ java -jar target/bcbio.variation-RELEASE-standalone.jar -T VariantAnnotator -A MeanNeighboringBaseQuality -R test/data/GRCh37.fa -I test/data/aligned-reads.bam --variant test/data/gatk-calls.vcf -o annotated-file.vcf
A YAML configuration file defines targets for comparison processing. Two example files for reference grading and comparison of calling methods provide example starting points and details on available options are below:
dir: base: Base directory to allow use of relative paths (optional). out: Working directory to write output. prep: Prep directory where files will be pre-processed. experiments: # one or more experiments - sample: Name of current sample. ref: Reference genome in FASTA format. intervals: Intervals to process in BED format (optional). align: Alignments for all calls in BAM format (optional). summary-level: Amount of summary information to provide, [full,quick] (default:full) params: # Processing parameters associated with this experiment max-indel: Maximum indel size to include in non-structural variant comparisons (default: 5000) multiple-thresh: Threshold for percentage of comparisons to match to consider two multiple sample variants the same. (default: 1.0) compare-approach: Provide alternative approaches to compare variants: approximate -- allow flexible matching of het/hom variants and indels recall-approach: Method to use for recalling variants: consensus -- Most common variant from multiple inputs approach: Type of comparison to do [compare,grade]. Default compare. calls: # two or more calls to compare - name: Name of call type file: One or more input files in VCF format align: Alignment for specific call in BAM format (optional). ref: Reference genome if different than experiment ref (optional) intervals: Genome intervals to process in BED format (optional). metadata: Dictionary of annotations associated with the call set. Finalizers use these to provide annotation specific filtering of calls. filters: Provide hard filtering of variants prior to comparison with specified JEXL GATK expressions. format-filters: Provide hard filtering of variants based on attributes in the genotype FORMAT field. recall: Recall variant positions after merging multiple input calls. Can tune with `recall-approach` in `params` (boolean; default false) annotate: Annotate calls with GATK annotations (boolean; default false). normalize: Normalize MNPs and indels (boolean: default true). prep: Prep with in-order chromosomes and sample names (boolean; default false). prep-sort-pos: Sort by position during prep. Required if variants are not coordinate sorted within chromosomes. (boolean; default false). fix-sample-header: Adjust VCF sample header names to match sample specified in `sample` (boolean; default false) prep-sv-genotype: Normalize structural variant genotypes to a single ref call (boolean; default false). prep-allele-count: Number of alleles to convert calls to during prep work (default 2) preclean: Remove problematic characters from input VCFs (boolean; default false). remove-refcalls: Remove reference, non-variant calls. (boolean; default false). make-haploid: Convert a set of diploid calls to haploid variants (boolean; default false)
In addition to the pairwise comparisons, the configuration allows specification
of additional filtration and all-by-all comparisons based on the pairwise
calls, specify these under an experiment with the
tag. Available methods are:
multiplewhich does a comparison of a target call method to all other calls. A comparison of GATK calls to all other methods looks like:
finalize: - method: multiple target: gatk ignore: 
and produces three output files:
- true positives -- calls detected in all methods
- false negatives -- calls not found in gatk, but detected in all other methods
- false positives -- calls found in gatk but callable and discordant in one of the other methods
ignoreoption provides a list of methods to ignore in the all-by-all overlap comparison.
recal-filterto do post-comparisons filtering of calls. This can use either the results of a pairwise comparison or
multiplecomparison. An example demonstrating all of the filtering options re-filters a GATK versus FreeBayes comparison:
finalize: - method: recal-filter target: [gatk, freebayes] params: filters: [HRun > 5.0] classifiers: [AD, DP, QUAL] xspecific: true trusted: total: 0.75 technology: 0.65 untrusted: total: 0.25
The options for filtering are:
filters-- Perform hard filtering of the file with specified expressions.
classifiers-- Perform classification of true/false reads based on the provided attributes.
trusted-- Metadata annotation values that specify trusted variants not subjected to filtering. The example retains variants present in more than 75% of calls or 65% of different technologies.
untrusted-- Specify threshold for variants that should be automatically filtered. The example excludes variants with support from less than 25% of the callers.
xspecific-- Identify and filter calls specific to a technology or calling method, when combining multiple callers and technologies.
You can specify the background to use for training with
support. There are two options:
support: gatk-- Use an all-by-all comparison based on GATK to establish true and false positives.
support: [gatk, freebayes]-- Use the gatk/freebayes pairwise comparison for true and false positives.
This library also contains useful command line utilities to help with variant preparation and analysis:
Create a BAM file compatible with GATK. This converts coordinates between hg19 and GRCh37 for human samples if needed, reorders chromosomes relative to the input file and adds run group information with a defined sample name:
$ lein variant-reorder your_file.bam /path/to/GRCh37.fa SampleName
Provide a summary CSV file of call information for a VCF file, including mappings back to an original set of pairwise analyses:
$ lein variant-utils callsummary variants.vcf original-combined-config.yaml
Sort a variant VCF file to reference ordering defined in a FASTA file
$ lein variant-utils sort-vcf variants.vcf reference.fa
Convert an Illumina directory of variant calls into a single, cleaned VCF:
$ lein variant-utils illumina /path/to/IlluminaDir sample-name GRCh37.fa hg19.fa
- Brad Chapman
- Chris Fields
- Kevin Lynagh
- Justin Zook
The code is freely available under the MIT license.