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freebayes, a haplotype-based variant detector

user manual and guide

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Overview

freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

freebayes is haplotype-based, in the sense that it calls variants based on the literal sequences of reads aligned to a particular target, not their precise alignment. This model is a straightforward generalization of previous ones (e.g. PolyBayes, samtools, GATK) which detect or report variants based on alignments. This method avoids one of the core problems with alignment-based variant detection--- that identical sequences may have multiple possible alignments:

<img src="https://github.com/freebayes/freebayes/raw/v1.3.0/paper/haplotype_calling.png" width=500/>

freebayes uses short-read alignments (BAM files with Phred+33 encoded quality scores, now standard) for any number of individuals from a population and a reference genome (in FASTA format) to determine the most-likely combination of genotypes for the population at each position in the reference. It reports positions which it finds putatively polymorphic in variant call file (VCF) format. It can also use an input set of variants (VCF) as a source of prior information, and a copy number variant map (BED) to define non-uniform ploidy variation across the samples under analysis.

freebayes is maintained by Erik Garrison and Pjotr Prins. See also RELEASE-NOTES.

Citing freebayes

A preprint Haplotype-based variant detection from short-read sequencing provides an overview of the statistical models used in freebayes. We ask that you cite this paper if you use freebayes in work that leads to publication. This preprint is used for documentation and citation. freebayes was never submitted for review, but has been used in over 1000 publications.

Please use this citation format:

Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012

If possible, please also refer to the version number provided by freebayes when it is run without arguments or with the --help option.

Install

freebayes is provided as a pre-built 64-bit static Linux binary as part of releases.

Debian and Conda packages should work too, see the badges at the top of this page.

To build freebayes from source check the development section below. It is important to get the full recursive git checkout and dependencies.

Support

Please report any issues or questions to the freebayes mailing list. Report bugs on the freebayes issue tracker

Usage

In its simplest operation, freebayes requires only two inputs: a FASTA reference sequence, and a BAM-format alignment file sorted by reference position. For instance:

freebayes -f ref.fa aln.bam >var.vcf

... will produce a VCF file describing all SNPs, INDELs, and haplotype variants between the reference and aln.bam. The CRAM version is

freebayes -f ref.fa aln.cram >var.vcf

Multiple BAM files may be given for joint calling.

Typically, we might consider two additional parameters. GVCF output allows us to have coverage information about non-called sites, and we can enable it with --gvcf. For performance reasons we may want to skip regions of extremely high coverage in the reference using the --skip-coverage parameter or -g. These can greatly increase runtime but do not produce meaningful results. For instance, if we wanted to exclude regions of 1000X coverage, we would run:

freebayes -f ref.fa aln.bam --gvcf -g 1000 >var.vcf

For a description of available command-line options and their defaults, run:

freebayes --help

Examples

Call variants assuming a diploid sample:

freebayes -f ref.fa aln.bam >var.vcf

Call variants on only chrQ:

freebayes -f ref.fa -r chrQ aln.bam >var.vcf

Call variants on only chrQ, from position 1000 to 2000:

freebayes -f ref.fa -r chrQ:1000-2000 aln.bam >var.vcf

Require at least 5 supporting observations to consider a variant:

freebayes -f ref.fa -C 5 aln.bam >var.vcf

Skip over regions of high depth by discarding alignments overlapping positions where total read depth is greater than 200:

freebayes -f ref.fa -g 200 aln.bam >var.vcf

Use a different ploidy:

freebayes -f ref.fa -p 4 aln.bam >var.vcf

Assume a pooled sample with a known number of genome copies. Note that this means that each sample identified in the BAM file is assumed to have 32 genome copies. When running with high --ploidy settings, it may be required to set --use-best-n-alleles to a low number to limit memory usage.

freebayes -f ref.fa -p 32 --use-best-n-alleles 4 --pooled-discrete aln.bam >var.vcf

Generate frequency-based calls for all variants passing input thresholds. You'd do this in the case that you didn't know the number of samples in the pool.

freebayes -f ref.fa -F 0.01 -C 1 --pooled-continuous aln.bam >var.vcf

Use an input VCF (bgzipped + tabix indexed) to force calls at particular alleles:

freebayes -f ref.fa -@ in.vcf.gz aln.bam >var.vcf

Generate long haplotype calls over known variants:

freebayes -f ref.fa --haplotype-basis-alleles in.vcf.gz \
                    --haplotype-length 50 aln.bam

Naive variant calling: simply annotate observation counts of SNPs and indels:

freebayes -f ref.fa --haplotype-length 0 --min-alternate-count 1 \
    --min-alternate-fraction 0 --pooled-continuous --report-monomorphic >var.vcf

Parallelisation

In general, freebayes can be parallelised by running multiple instances of freebayes on separate regions of the genome, and then concatenating the resulting output. The wrapper, freebayes-parallel will perform this, using GNU parallel.

Example freebayes-parallel operation (use 36 cores in this case):

freebayes-parallel <(fasta_generate_regions.py ref.fa.fai 100000) 36 \
    -f ref.fa aln.bam > var.vcf

Note that any of the above examples can be made parallel by using the scripts/freebayes-parallel script. If you find freebayes to be slow, you should probably be running it in parallel using this script to run on a single host, or generating a series of scripts, one per region, and run them on a cluster. Be aware that the freebayes-parallel script contains calls to other programs using relative paths from the scripts subdirectory; the easiest way to ensure a successful run is to invoke the freebayes-parallel script from within the scripts subdirectory.

A current limitation of the freebayes-parallel wrapper, is that due to variance in job memory and runtimes, some cores can go unused for long periods, as they will not move onto the next job unless all cores in use have completed their respective genome chunk. This can be partly avoided by calculating coverage of the input bam file, and splitting the genome into regions of equal coverage using the coverage_to_regions.py script. An alternative script split_ref_by_bai_datasize.py will determine target regions based on the data within multiple bam files, with the option of choosing a target data size. This is useful when submitting to Slurm and other cluster job managers, where use of resources needs to be controlled.

Alternatively, users may wish to parallelise freebayes within the workflow manager snakemake. As snakemake automatically dispatches jobs when a core becomes available, this avoids the above issue. An example .smk file, and associated conda environment recipe, can be found in the /examples directory.

Calling variants: from fastq to VCF

You've sequenced some samples. You have a reference genome or assembled set of contigs, and you'd like to determine reference-relative variants in your samples. You can use freebayes to detect the variants, following these steps:

freebayes emits a standard VCF 4.1 output stream. This format is designed for the probabilistic description of allelic variants within a population of samples, but it is equally suited to describing the probability of variation in a single sample.

Of primary interest to most users is the QUAL field, which estimates the probability that there is a polymorphism at the loci described by the record. In freebayes, this value can be understood as 1 - P(locus is homozygous given the data). It is recommended that users use this value to filter their results, rather than accepting anything output by freebayes as ground truth.

By default, records are output even if they have very low probability of variation, in expectation that the VCF will be filtered using tools such as vcffilter in vcflib, which is also included in the repository under vcflib/. For instance,

freebayes -f ref.fa aln.bam | vcffilter -f "QUAL > 20" >results.vcf

removes any sites with estimated probability of not being polymorphic less than phred 20 (aka 0.01), or probability of polymorphism > 0.99.

In simulation, the receiver-operator characteristic (ROC) tends to have a very sharp inflection between Q1 and Q30, depending on input data characteristics, and a filter setting in this range should provide decent performance. Users are encouraged to examine their output and both variants which are retained and those they filter out. Most problems tend to occur in low-depth areas, and so users may wish to remove these as well, which can also be done by filtering on the DP flag.

Calling variants in a population

freebayes is designed to be run on many individuals from the same population (e.g. many human individuals) simultaneously. The algorithm exploits a neutral model of allele diffusion to impute most-confident genotypings across the entire population. In practice, the discriminant power of the method will improve if you run multiple samples simultaneously. In other words, if your study has multiple individuals, you should run freebayes against them at the same time. This also ensures consistent reporting of information about evidence for all samples at any locus where any are apparently polymorphic.

To call variants in a population of samples, each alignment must have a read group identifier attached to it (RG tag), and the header of the BAM file in which it resides must map the RG tags to sample names (SM). Furthermore, read group IDs must be unique across all the files used in the analysis. One read group cannot map to multiple samples. The reason this is required is that freebayes operates on a virtually merged BAM stream provided by the BamTools API. If merging the files in your analysis using bamtools merge would generate a file in which multiple samples map to the same RG, the files are not suitable for use in population calling, and they must be modified.

Users may add RG tags to BAM files which were generated without this information by using (as mentioned in "Calling variants" above) bamaddrg. If you have many files corresponding to many individuals, add a unique read group and sample name to each, and then open them all simultaneously with freebayes. The VCF output will have one column per sample in the input.

Performance tuning

If you find freebayes to be slow, or use large amounts of memory, consider the following options:

Observation filters and qualities

Input filters

By default, freebayes doesn't

freebayes may be configured to filter its input so as to ignore low-confidence alignments and alleles which are only supported by low-quality sequencing observations (see --min-mapping-quality and --min-base-quality). It also will only evaluate a position if at least one read has mapping quality of --min-supporting-mapping-quality and one allele has quality of at least --min-supporting-base-quality.

Reads with more than a fixed number of high-quality mismatches can be excluded by specifying --read-mismatch-limit. This is meant as a workaround when mapping quality estimates are not appropriately calibrated.

Reads marked as duplicates in the BAM file are ignored, but this can be disabled for testing purposes by providing --use-duplicate-reads. freebayes does not mark duplicates on its own, you must use another process to do this, such as that in sambamba.

Observation thresholds

As a guard against spurious variation caused by sequencing artifacts, positions are skipped when no more than --min-alternate-count or --min-alternate-fraction non-clonal observations of an alternate are found in one sample. These default to 2 and 0.05 respectively. The default setting of --min-alternate-fraction 0.05 is suitable for diploid samples but may need to be changed for higher ploidy.

Allele type exclusion

freebayes provides a few methods to ignore certain classes of allele, e.g. --throw-away-indels-obs and --throw-awary-mnps-obs. Users are strongly cautioned against using these, because removing this information is very likely to reduce detection power. To generate a report only including SNPs, use vcffilter post-call as such:

freebayes ... | vcffilter -f "TYPE = snp"

Normalizing variant representation

If you wish to obtain a VCF that does not contain haplotype calls or complex alleles, first call with default parameters and then decompose the output with tools in vcflib, vt, vcf-tools, bcftools, GATK, or Picard. Here we use a tool in vcflib that normalizes the haplotype calls into pointwise SNPs and indels:

freebayes ... | vcfallelicprimitives -kg >calls.vcf

Note that this is not done by default as it makes it difficult to determine which variant calls freebayes completed. The raw output faithfully describes exactly the calls that were made.

Observation qualities

freebayes estimates observation quality using several simple heuristics based on manipulations of the phred-scaled base qualities:

By default, both base and mapping quality are into the reported site quality (QUAL in the VCF) and genotype quality (GQ, when supplying --genotype-qualities). This integration is driven by the "Effective Base Depth" metric first developed in snpTools, which scales observation quality by mapping quality: P(Obs|Genotype) ~ P(MappedCorrectly(Obs))P(SequencedCorrectly(Obs)). Set --standard-gls to use the model described in the freebayes preprint.

Stream processing

freebayes can read BAM from standard input --stdin instead of directly from files. This allows the application of any number of streaming BAM filters and calibrators to its input.

bam_merger.sh | streaming_filter_or_process.sh | freebayes --stdin ...

This pattern allows the adjustment of alignments without rewriting BAM files, which could be expensive depending on context and available storage. A prime example of this would be graph-based realignment of reads to known variants as implemented in glia.

Using this pattern, you can filter out reads with certain criteria using bamtools filter without having to modify the input BAM file. You can also use the bamtools API to write your own custom filters in C++. An example filter is bamfiltertech [src/bamfiltertech.cpp](http://github.com/freebayes/freebayes/blob/master/src/bamfilte rtech.cpp), which could be used to filter out technologies which have characteristic errors which may frustrate certain types of variant detection.

INDELs

In principle, any gapped aligner which is sensitive to indels will produce satisfactory input for use by freebayes. Due to potential ambiguity, indels are not parsed when they overlap the beginning or end of alignment boundaries.

When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. This is now done automatically by freebayes, but the behavior can be turned off via --dont-left-align-indels flag. You probably don't want to do this.

Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method computationally inexpensive and handles the most common classes of alignment inconsistency.

Haplotype calls

As freebayes is haplotype-based, left-alignment is necessary only for the determination of candidate polymorphic loci. Once such loci are determined, haplotype observations are extracted from reads where:

  1. putative variants lie within --haplotype-length bases of each other (default 3bp),
  2. the reference sequence has repeats (e.g. microsatellites or STRs are called as one haplotype),
  3. the haplotype which is called has Shannon entropy less than --min-repeat-entropy, which is off by default but can be set to ~1 for optimal genotyping of indels in lower-complexity sequence.

After a haplotype window is determined by greedily expanding the window across overlapping haplotype observations, all reads overlapping the window are used to establish data likelihoods, P(Observations|Genotype), for all haplotypes which have sufficient support to pass the input filters.

Partial observations are considered to support those haplotypes which they could match exactly. For expedience, only haplotypes which are contiguously observed by the reads are considered as putative alleles in this process. This differs from other haplotype-based methods, such as Platypus, which consider all possible haplotypes composed of observed component alleles (SNPs, indels) in a given region when generating likelihoods.

The primary adantages of this approach are conceptual simplicity and performance, and it is primarily limited in the case of short reads, an issue that is mitigated by increasing read lengths. Also, a hybrid approach must be used to call haplotypes from high-error rate long reads.

Re-genotyping known variants and calling long haplotypes

For longer reads with higher error rates, it is possible to generate long haplotypes in two passes over the data. For instance, if we had very long reads (e.g. >10kb) at moderate depth and high error rate (>5%) such as might be produced by PacBio, we could do something like:

freebayes -f ref.fa aln.bam | vcffilter -f "QUAL > 20" >vars.vcf

... thus generating candidate variants of suitable quality using the default detection window. We can then use these as "basis alleles" for the observation of haplotypes, considering all other putative variants supported by the alignment to be sequencing errors:

freebayes -f ref.fa --haplotype-length 500 \
    --haplotype-basis-alleles vars.vcf aln.bam >haps.vcf

These steps should allow us to read long haplotypes directly from input data with high error rates.

The high error rate means that beyond a small window each read will contain a completely different literal haplotype. To a point, this property improves our signal to noise ratio and can effectively filter out sequencing errors at the point of the input filters, but it also decreases the effective observation depth will prevent the generation of any calls if a long --haplotype-length is combined with high a sequencing error rate.

Best practices and design philosophy

freebayes follows the patterns suggested by the Unix philosophy, which promotes the development of simple, modular systems that perform a single function, and can be combined into more complex systems using stream processing of common interchange formats.

freebayes incorporates a number of features in order to reduce the complexity of variant detection for researchers and developers:

A minimal pre-processing pipeline similar to that described in "Calling variants" should be sufficient for most uses. For more information, please refer to a post by Brad Chapman on minimal BAM preprocessing methods.

Development

To download freebayes, please use git to download the most recent development tree:

git clone --recursive https://github.com/freebayes/freebayes.git

If you have a repo, update the submodules with

git submodule update --init --recursive --progress

On Debian you'll need a gcc compiler and want packages:

Build dependencies are listed in guix.scm and travis. Builds have been tested with gcc 7 and clang 9.

Compilation

Make sure to have dependencies installed and checkout the tree with --recursive.

Freebayes can target AMD64 and ARM64 (with Neon extensions).

Recently we added the meson build system which can be run with

meson build/ --buildtype release

For development/debugging use

meson build/ --buildtype debug

or to setup with clang instead

env CXX=clang++ CC=clang CC_LD=lld meson build --buildtype debug

Next compile and test in the build directory

cd build
ninja
ninja test

The freebayes binary should be in

build/freebayes

Tests on ARM may be slow. If you get a TIMEOUT use a multiplier, e.g.

meson test -t 4 -C build/

See meson.build for more information.

Compile in a Guix container

After checking out the repo with git recursive create a Guix container with all the build tools with

guix shell -C -D -f guix.scm

See also the header of guix.scm.