Freebayes

https://github.com/ekg/freebayes

freebayes, a haplotype-based variant detector

user manual and guide

Erik Garrison erik.garrison@bc.edu

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:

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.

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.

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. For example, you should see something like this:

version:  v0.9.10-3-g47a713e-dirty

This provides both a point release number and a git commit id, which will ensure precise reproducibility of results.

Obtaining

To download FreeBayes, please use git to download the most recent development tree. Currently, the tree is hosted on github, and can be obtained via:

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

Note the use of --recursive. This is required in order to download all nested git submodules for external repositories.

After you've already done the above to clone the most recent development version, if you wish to compile a specific version of FreeBayes from, you can then do:

git checkout v0.9.18 && git submodule update --recursive

Resolving proxy issues with git

Depending on your local network configuration, you may have problems obtaining freebayes via git. If you see something like this you may be behind a proxy that blocks access to standard git:// port (9418).

$ git clone --recursive git://github.com/ekg/freebayes.git
Cloning into 'freebayes'...
fatal: Unable to look up github.com (port 9418) (Name or service not known)

Luckily, if you have access to https:// on port 443, then you can use this 'magic' command as a workaround to enable download of the submodules:

git config --global url.https://github.com/.insteadOf git://github.com/

Compilation

FreeBayes requires g++ and the standard C and C++ development libraries. Additionally, cmake is required for building the BamTools API.

make

Will build the executable freebayes, as well as the utilities bamfiltertech and bamleftalign. These executables can be found in the bin/ directory in the repository.

Users may wish to install to e.g. /usr/local/bin (default), which is accomplished via

sudo make install

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 --fasta-reference h.sapiens.fasta NA20504.bam

... produce (on standard output) a VCF file on standard out describing all SNPs, INDELs, MNPs, and Complex events between the reference and the alignments in NA20504.bam. In order to produce correct output, the reference supplied must be the reference to which NA20504.bam was aligned.

Users may specify any number of BAM files on the command line. FreeBayes uses the BamTools API to open and parse these files in parallel, virtually merging them at runtime into one logical file with a merged header.

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

freebayes --help

Calling variants

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:

Align your reads to a suitable reference (e.g. with bwa or MOSAIK)
Ensure your alignments have read groups attached so their sample may be identified by freebayes. Aligners allow you to do this, but you can also use bamaddrg to do so post-alignment.
Sort the alignments (e.g. bamtools sort).
Mark duplicates, for instance with samtools rmdup (if PCR was used in the preparation of your sequencing library)
Run freebayes on all your alignment data simultaneously, generating a VCF. The default settings should work for most use cases, but if your samples are not diploid, set the --ploidy and adjust the --min-alternate-fraction suitably.
Filter the output e.g. using reported QUAL and/or depth (DP) or observation count (AO).
Interpret your results.
(possibly, Iterate the variant detection process in response to insight gained from your interpretation)

FreeBayes a standard VCF 4.1 outut 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.

Observation filters and qualities

Input filters

FreeBayes filters 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.

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 0.2 respectively. The default setting of --min-alternate-fraction 0.2 is suitable for diploid samples but should be changed for ploidy > 2.

Allele type exclusion

FreeBayes provides a few methods to ignore certain classes of allele, e.g. --no-indels and --no-mnps. 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"

Observation qualities

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

For single-base observations, mismatches and reference observations: the un-adjusted base quality provided in the BAM alignment record.
For insertions: the mean quality of the bases inside of the putatively inserted sequence.
For deletions: the mean quality of the bases flanking the putatively deleted sequence.
For haplotypes: the mean quality of allele observations within the haplotype.

Effective base depth

By default, filters are left completely open, as both mapping quality and base quality are incorporated 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. In short, P(Obs|Genotype) ~ P(MappedCorrectly(Obs))P(SequencedCorrectly(Obs)).

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, 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:

putative variants lie within --haplotype-window bases of each other (default 3bp),
the reference sequence has repeats (e.g. microsatellites or STRs are called as one haplotype),
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-window 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-window 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:

Indel realignment is accomplished internally using a read-independent method, and issues resulting from discordant alignments are dramatically reducedy through the direct detection of haplotypes.
The need for base quality recalibration is avoided through the direct detection of haplotypes. Sequencing platform errors tend to cluster (e.g. at the ends of reads), and generate unique, non-repeating haplotypes at a given locus.
Variant quality recalibration is avoided by incorporating a number of metrics, such as read placement bias and allele balance, directly into the Bayesian model. (Our upcoming publication will discuss this in more detail.)

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 recent post by Brad Chapman on minimal BAM preprocessing methods.

For a push-button solution to variant detection, from reads to variant calls, look no further than the gkno genome analysis platform.

Support

Please report any issues or questions to the freebayes mailing list, freebayes issue tracker, or by email to erik.garrison@bc.edu.

Note that if you encounter issues with the development HEAD and you would like a quick workaround for an issue that is likely to have been reintroduced recently, you can use git checkout to step back a few revisions.

git checkout [git-commit-id]

It will also help with debugging to know if a problem has arisen in recent commits!