Folks, I’m all out of banter for this one, so let’s go straight to the facts. GATK 3.4 contains a shedload of improvements and bug fixes, including some new functionality that we hope you’ll find useful. The full list is available in the detailed release notes.
None of the recent changes involves any disruption to the Best Practice workflow (I hear some sighs of relief) but you’ll definitely want to check out the tweaks we made to the joint discovery tools (HaplotypeCaller, CombineGVCFs and GenotypeGVCFs), which are rapidly maturing as they log more flight time at Broad and in the wild.
Let’s start at the very beginning with HaplotypeCaller (a very good place to start). On the usability front, we’ve finally given in to the nigh-universal complaint about the required variant indexing arguments (
--variant_index_type LINEAR --variant_index_parameter 128000) being obnoxious and a waste of characters. So, tadaa, they are no longer required, as long as you name your output file with the extension
.g.vcf so that the engine knows what level of compression to use to write the gVCF index (which leads to better performance in downstream tools). We think this naming convention makes a lot of sense anyway, as it’s a great way to distinguish gVCFs from regular VCFs on sight, so we hope most of you will adopt it. That said, we stopped short of making this convention mandatory (for now…) so you don’t have to change all your scripts and conventions if you don’t want to. All that will happen (assuming you still specify the variant index parameters as previously) is that you’ll get a warning in the log telling you that you could use the new convention.
Where we’ve been a bit more dictatorial is that we’ve completely disabled the use of
-dcov with HaplotypeCaller because it was causing very buggy behavior due to an unforeseen complication in how different levels of downsampling are applied in HaplotypeCaller. We know that the default setting does the right thing, and there’s almost no legitimate reason to change it, so we’re disabling this for the greater good pending a fix (which may be a long time coming due to the complexity of the code involved).
Next up, CombineGVCFs gets a new option to break up reference blocks at every N sites. The new argument
--breakBandsAtMultiplesOf Nwill ensure that no reference blocks in the combined gVCF span genomic positions that are multiples of N. This is meant to enable scatter-gather parallelization of joint genotyping on whole-genome data, as a workaround to some annoying limitations of the GATK engine that make it unsafe to use
-L intervals that might start within the span of a block record. For exome data, joint genotyping can easily be parallelized by scatter-gathering across exome capture target intervals, because we know that there won’t be any hom-ref block records spanning the target interval boundaries. In contrast, in whole-genome data, there is no equivalent predictable termination of block records, so it’s not possible to know up front where it would be safe to set scatter-gather interval start and end points -- until now!
And finally, GenotypeGVCFs gets an important bug fix, and a very useful new annotation.
The bug is something that has arisen mostly (though not exclusively) from large cohort studies. What happened is that, when a SNP occurred in sample A at a position that was in the middle of a deletion for sample B, GenotypeGVCFs would emit a homozygous reference genotype for sample B at that position -- which is obviously incorrect. The fix is that now, sample B will be genotyped as having a symbolic
<DEL> allele representing the deletion.
The new annotation is called
RGQ for Reference Genotype Quality. It is a new sample-level annotation that will be added by GenotypeGVCFs to monomorphic sites if you use the
-allSites argument to emit non-variant sites to the output VCF. This is obviously super useful for evaluating the level of confidence of those sites called homozygous-reference.
This new coverage analysis tool is designed to count read depth in a way that is appropriate for allele-specific expression (ASE) analysis. It counts the number of reads that support the REF allele and the ALT allele, filtering low qual reads and bases and keeping only properly paired reads. The default output format produced by this tool is a structured text file intended to be consumed by the statistical analysis toolkit MAMBA. A paper by Stephane Castel and colleagues describing the complete ASE analysis workflow is available as a preprint on bioarxiv.
We’ve added two new documentation resources to the Guide.
One is a new category of documentation articles called Common Problems, to cover topics that are a specialized subset of FAQs: problems that many users encounter, which are typically due to misunderstandings about input requirements or about the expected behavior of the tools, or complications that arise from certain experimental designs. This category is being actively worked on and we welcome suggestions of additional topics that it should cover.
The second is an Issue Tracker that lists issues that have been reported as well as features or enhancements that have been requested. If you encounter a problem that you think might be a bug (or you have a feature request in mind), you can check this page to see if it’s something we already know about. If you have submitted a bug report, you can use the issue tracker to check whether your issue is in the backlog, in the queue, or is being actively worked on. In future we’ll add some functionality to enable voting on what issues or features should be prioritized, so stay tuned for an announcement on that!
Another season, another GATK release. Personally, Fall is my favorite season, and while I don’t want to play favorites with versions (though unlike with children, you’re allowed to say that the most recent one is the best --and you can tell I was a youngest child) this one is pretty special to me.
-ploidy! Yeah, that’s really all I need to say about that. I was a microbiologist once. And I expect many plant people will be happy too.
Other cool stuff detailed below includes: full functionality for the genotype refinement workflow tools; physical phasing and appropriate handling of dangly bits by HaplotypeCaller (must… resist… jokes…); a wealth of new documentation for variant annotations; and a slew of bug fixes that I won’t go over but are listed in the release notes.
As announced earlier this week, we recently developed a workflow for refining genotype calls, intended for researchers who need highly accurate genotype information as well as preliminary identification of possible de novo mutations (see the documentation for details). Although all the tools involved were already available in GATK 3.2, some functionalities were not, so we’re very happy to finally make all of them available in this new version. Plus, we like the new StrandOddsRatio annotation (which sort of replaces FisherStrand for estimating strand bias) so much that we made it a standard one, and it now gets annotated by default.
This is also a feature that was announced a little while ago, but until now was only fully available in the nightly builds, which are technically unsupported unless we tell you to use them to get past a bad bug. In this new release, both HaplotypeCaller and GenotypeGVCFs are able to deal with non-diploid organisms (whether haploid or exotically polyploid). In the case of HaplotypeCaller, you need to specify the ploidy of your non-diploid sample with the
-ploidy argument. HC can only deal with one ploidy at a time, so if you want to process different chromosomes with different ploidies (e.g. to call X and Y in males) you need to run them separately. On the bright side, you can combine the resulting files afterward. In particular, if you’re running the
-ERC GVCF workflow, you’ll find that both CombineGVCFs and GenotypeGVCFs are able to handle mixed ploidies (between locations and between samples). Both tools are able to correctly work out the ploidy of any given sample at a given site based on the composition of the GT field, so they don’t require you to specify the
You know how HC performs a complete reassembly of reads in an ActiveRegion? (If you don’t, go read this now. Go on, we’ll wait for you.) Well, this involves building an assembly graph, of course (of course!), and it produces a list of haplotypes. Fast-forward a couple of steps, and you end up with a list of variants. That’s great, but until now, those variants were unphased, meaning the HC didn’t give you any information about whether any two variants’ alleles were on the same haplotype (meaning, on the same physical piece of DNA) or not. For example, you’d want to know whether you had this:
But HC wouldn’t tell you which it was in its output. Which was a shame, because the HC sees that information! It took a little tweaking to get it to talk, but now it emits physical phasing by default in its GVCF output (both banded GVCF and BP_RESOLUTION).
In a nutshell, phased records will look like this:
1 1372243 . T <NON_REF> . . END=1372267 <snip> <snip> 1 1372268 . G A,<NON_REF> . . <snip> GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:30,40,0:70:99:0|1:1372268_G_A:<snip> 1 1372269 . G T,<NON_REF> . . <snip> GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:30,41,0:71:99:0|1:1372268_G_A:<snip> 1 1372270 . C <NON_REF> . . END=1372299 <snip> <snip>
You see that the phasing info is encoded in two new sample-level annotations, PID (for phase identifier) and PGT (phased genotype). More than two variants can be phased in a group with the same PID, and that can include mixed types of variants (e.g. SNPs and indels).
The one big caveat related to the physical phasing output by HC in GVCFs is that, like the GVCF itself, it is not intended to be used directly for analysis! You must run your GVCFs through GenotypeGVCFs in order to get the finalized, properly formatted, ready-for-analysis calls.
Speaking of HaplotypeCaller getting more helpful all the time, here’s some more of that. This still has to do with the graph assembly, and specifically, with how HC handles the bits at the edges of the graph, which are called dangling heads and dangling tails. Without going too far into the details, let’s just say that sometimes you have a variant that’s near the edge of a covered region, and due to technical reasons (cough kmer size cough) the end of the variant path can’t be tied back into the reference path, so it just dangles there (like, say, Florida) and gets trimmed off in the next step (rising ocean levels). And thus the variant is lost (boo).
We originally started paying attention to this because it often happens at the edge of exons near splice junctions in RNAseq data, but it can also happen in DNA data. The solution was to give HC the ability to recover these cliff-dwelling variants by merging the dangling ends back into the graph using special logic tailored for those situations. If you have been using our RNAseq Best Practices, then you may recognize this as the logic invoked by the
--recoverDanglingHeads argument. In the new version, the functionality has been improved further and is now enabled by default for all variant calling (so you no longer need to specify that argument for RNAseq analysis). The upshot is that sensitivity is improved, especially for RNAseq data but also for DNA.
Finally, I want to attract everyone’s attention to the Variant Annotations section of the Tool Documentation, which has just undergone a comprehensive overhaul. All annotations now have some kind of documentation outlining their general purpose, output, interpretation, caveats and some notes about how they’re calculated where applicable. Tell us what you think; we are feedback junkies.
Better late than never (right?), here are the version highlights for GATK 3.2. Overall, this release is essentially a collection of bug fixes and incremental improvements that we wanted to push out to not keep folks waiting while we're working on the next big features. Most of the bug fixes are related to the HaplotypeCaller and its "reference confidence model" mode (which you may know as
-ERC GVCF). But there are also a few noteworthy improvements/changes in other tools which I'll go over below.
The "reference confidence model" workflow, which I hope you have heard of by now, is that awesome new workflow we released in March 2014, which was the core feature of the GATK 3.0 version. It solves the N+1 problem and allows you to perform joint variant analysis on ridiculously large cohorts without having to enslave the entire human race and turning people into batteries to power a planet-sized computing cluster. More on that later (omg we're writing a paper on it, finally!).
You can read the full list of improvements we've made to the tools involved in the workflow (mainly HaplotypeCaller and Genotype GVCFs) in Eric's (unusually detailed) Release Notes for this version. The ones you are most likely to care about are that the "missing PLs" bug is fixed, GenotypeGVCFs now accepts arguments that allow it to emulate the HC's genotyping capabilities more closely (such as
--includeNonVariantSites), the AB annotation is fully functional, reference DPs are no longer dropped, and CatVariants now accepts lists of VCFs as input. OK, so that last one is not really specific to the reference model pipeline, but that's where it really comes in handy (imagine generating a command line with thousands of VCF filenames -- it's not pretty).
The coverage metrics (DP and AD) reported by HaplotypeCaller are now those calculated after the HC's reassembly step, based on the reads having been realigned to the most likely haplotypes. So the metrics you see in the variant record should match what you see if you use the
-bamout option and visualize the reassembled ActiveRegion in a genome browser such as IGV. Note that if any of this is not making sense to you, say so in the comments and we'll point you to the new HaplotypeCaller documentation! Or, you know, look for it in the Guide.
We updated the plotting scripts used by BQSR and VQSR to use the latest version of ggplot2, to get rid of some deprecated function issues. If your Rscripts are suddenly failing, you'll need to update your R libraries.
We're sorry for making you jump through all these hoops recently. As if the switch to Maven wasn't enough, we have now completed a massive reorganization/renaming of the codebase that will probably cause you some headaches when you port your tools to the newest version. But we promise this is the last big wave, and ultimately this will make your life easier once we get the GATK core framework to be a proper maven artifact.
In a nutshell, the base name of the codebase has changed from
gatk (which hopefully makes more sense), and the most common effect is that
sting.gatk classpath segments are now
gatk.tools. This, by the way, is why we had a bunch of broken documentation links; most of these have been fixed (yay symlinks) but there may be a few broken URLs remaining. If you see something, say something, and we'll fix it.
This may seem crazy considering we released the big 3.0 version not two weeks ago, but yes, we have a new version for you already! It's a bit of a special case because this release is all about the hardware-based optimizations we had previously announced. What we hadn't announced yet was that this is the fruit of a new collaboration with a team at Intel (which you can read more about here), so we were waiting for everyone to be ready for the big reveal.
So basically, the story is that we've started collaborating with the Intel Bio Team to enable key parts of the GATK to run more efficiently on certain hardware configurations. For our first project together, we tackled the PairHMM algorithm, which is responsible for a large proportion of the runtime of HaplotypeCaller analyses. The resulting optimizations, which are the main feature in version 3.1, produce significant speedups for HaplotypeCaller runs on a wide range of hardware.
We will continue working with Intel to further improve the performance of GATK tools that have historically been afflicted with performance issues and long runtimes (hello BQSR). As always, we hope these new features will make your life easier, and we welcome your feedback in the forum!
Note that these optimizations currently work on Linux systems only, and will not work on Mac or Windows operating systems. In the near future we will add support for Mac OS. We have no plans to add support for Windows since the GATK itself does not run on Windows.
Please note also that to take advantage of these optimizations, you need to opt-in by adding the following flag to your GATK command:
Here is a handy little table of the speedups you can expect depending on the hardware and operating system you are using. The configurations given here are the minimum requirements for benefiting from the expected speedup ranges shown in the third column. Keep in mind that these numbers are based on tests in controlled conditions; in the wild, your mileage may vary.
|Linux kernel version||Architecture / Processor||Expected speedup||Instruction set|
|Any 64-bit Linux||Any x86 64-bit||1-1.5x||Non-vector|
|Linux 2.6 or newer||Penryn (Core 2 or newer)||1.3-1.8x||SSE 4.1|
|Linux 2.6.30 or newer||SandyBridge (i3, i5, i7, Xeon E3, E5, E7 or newer)||2-2.5x||AVX|
To find out exactly which processor is in your machine, you can run this command in the terminal:
$ cat /proc/cpuinfo | grep "model name" model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz model name : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
In this example, the machine has 4 cores (8-threads), so you see the answer 8 times. With the model name (here i7-2600) you can look up your hardware's relevant capabilities in the Wikipedia page on vector extensions.
Alternatively, Intel has provided us with some links to lists of processors categorized by architecture, in which you can look up your hardware:
Finally, a few notes to clarify some concepts regarding Linux kernels vs. distributions and processors vs. architectures:
SandyBridge and Penryn are microarchitectures; essentially, these are sets of instructions built into the CPU. Core 2, core i3, i4, i7, Xeon e3, e5, e7 are the processors that will implement a specific architecture to make use of the relevant improvements (see table above).
The Linux kernel has no connection with Linux distribution (e.g. Ubuntu, RedHat etc). Any distribution can use any kernel they want. There are "default kernels" shipped with each distribution, but that's beyond the scope of this article to cover (there are at least 300 Linux distributions out there). But you can always install whatever kernel version you want.
The kernel version 2.6.30 was released in 2009, so we expect every sane person or IT out there to be using something better than this.
Better late than never, here is the now-traditional "Highlights" document for GATK version 3.0, which was released two weeks ago. It will be a very short one since we've already gone over the new features in detail in separate articles --but it's worth having a recap of everything in one place. So here goes.
We are delighted to present our new Best Practices workflow for variant calling in which multisample calling is replaced by a winning combination of single-sample calling in gVCF mode and joint genotyping analysis. This allows us to both bypass performance issues and solve the so-called "N+1 problem" in one fell swoop. For full details of why and how this works, please see this document. In the near future, we will update our Best Practices page to make it clear that the new workflow is now the recommended way to go for calling variants on cohorts of samples. We've already received some pretty glowing feedback from early adopters, so be sure to try it out for yourself!
All the cool kids were doing it, so we had to join the party. It took a few months of experimentation, a couple of new tools and some tweaks to the HaplotypeCaller, but you can now call variants on RNAseq with GATK! This document details our Best Practices recommendations for doing so, along with a non-trivial number of caveats that you should keep in mind as you go.
Nice try, but no. This tool is obsolete now that we have the gVCF/reference model pipeline (see above). Note that this means that GATK 3.0 will not support BAM files that were processed using ReduceReads!
We've switched the build system from Ant to Maven, which should make it much easier to use GATK as a library against which you can develop your own tools. And on a related note, we're also making significant changes to the internal structure of the GATK codebase. Hopefully this will not have too much impact on external projects, but there will be a doc very shortly describing how the new build system works and how the codebase is structured.
For reasons that will be made clear in the near future, we decided to hold the previously announced hardware optimizations until version 3.1, which will be released very soon. Stay tuned!
Better late than never, here are the highlights of the most recent version release, GATK 2.8. This should be short and sweet because as releases go, 2.8 is light on new features, and is best described as a collection of bug fixes, which are all* dutifully listed in the corresponding release notes document. That said, two of the changes we've made deserve some additional explanation.
* Up to now (this release included) we have not listed updates/patches to Queue in the release notes, but will start doing so from the next version onward.
In the last release (2.7, for those of you keeping score at home) we trumpeted that the old
-percentBad argument of VariantRecalibrator had been replaced by the shiny new
-numBad argument, and that this was going to be awesome for all sorts of good reasons, improve stability and whatnot. Weeeeeeell it turned out that wasn't quite the case. It worked really well on the subset of analyses that we tested it on initially, but once we expanded to different datasets (and the complaints started rolling in on the forum) we realized that it actually made things worse in some cases because the default value was less appropriate than what
-percentBad would have produced. This left people guessing as to what value would work for their particular dataset, with a great big range to choose from and very little useful information to assist in the choice.
So, long story short, we (and by "we" I mean Ryan) built in a new function that allows the VariantRecalibrator to determine for itself the amount of variants that is appropriate to use for the "bad" model depending on the data. So the short-lived
-numBad argument is gone too, replaced by... nothing. No new argument to specify; just let the VariantRecalibrator do its thing.
Of course if you really want to, you can override the default behavior and tweak the internal thresholds. See the tool doc here; and remember that a good rule of thumb is that if you can't figure out which arguments are involved based on that doc, you probably shouldn't be messing with this advanced functionality.
This is still a rather experimental feature, so we're still making changes as we go. The two big changes worth mentioning here are that you can now run this on reduced reads, and that we've changed the indexing routine to optimize the compression level. The latter shouldn't have any immediate impact on normal users, but it was necessary for a new feature project we've been working on behind the scenes (the single-sample-to-joint-discovery pipeline we have been alluding to in recent forum discussions). The reason we're mentioning it now is that if you use
-ERC GVCF output, you'll need to specify a couple of new arguments as well (
-variant_index_type LINEAR and
-variant_index_parameter 128000, with those exact values). This useful little fact didn't quite make it into the documentation before we released, and not specifying them leads to an error message, so... there you go. No error message for you!
That's all for tool changes. In addition to those, we have made a number of corrections in the tool documentation pages, updated the Best Practices (mostly layout, tiny bit of content update related to the VQSR -numBad deprecation) and made some minor changes to the website, e.g. updated the list of publications that cite the GATK and improved the Guide index somewhat (but that's still a work in progress).
Yay, August is over! Goodbye steamy hot days, hello mild temperatures and beautiful leaf-peeping season. We hope you all had a great summer (in the Northern hemisphere at least) and caught a bit of a vacation. For our part, we've been chained to our desks the whole time!
Well, not really, but we've got a feature-rich release for you nonetheless. Lots of new things; not all of them fully mature, so heed the caveats on the experimental features! We've also made some key improvements to VQSR that we're very excited about, some bug fixes to various tools of course, and a new way to boost calling performance. Full list in the release notes as usual, and highlights below.
When UnifiedGenotyper and HaplotypeCaller emit variant calls, they tell you how confident you can be that the variants are real. But how do you know how confident to be that the rest are reference, i.e. non-variant? It's actually a pretty hard problem… and this is our answer:
For HaplotypeCaller, we’ve developed a full-on reference model that produces reference confidence scores. To use it, you need to enable the
--emitRefConfidence mode. This mode is a little bit complicated so be sure you read the method article before you try to use it.
For UnifiedGenotyper, we don’t have a completely fleshed-out model, but we’ve added the
-allSitePLs argument which, in combination with the
EMIT_ALL_SITES output mode, will enable calculation of PLs for all sites, including reference. This will give a measure of reference confidence and a measure of which alt alleles are more plausible (if any). Note that this only works with the SNP calling model. Again, this is not as good or as complete as the reference model in HaplotypeCaller, so we urge you to use HaplotypeCaller for this unless you really need to use UnifiedGenotyper.
These are two highly experimental features; they work in our tests, but your mileage may vary, so please examine your results carefully. We welcome your feedback!
A common problem in calling indels is that you get false positives that are associated with PCR slippage around short tandem repeats (especially homopolymers). Until we can all switch to PCR-free amplification, we're stuck with this issue. So we thought it would be nice to be able to model this type of error and mitigate its impact on our indel calls. The new
--pcr_indel_model argument allows the HaplotypeCaller to use a new feature called the PCR indel model to weed out false positive indels more or less aggressively depending on how much you care about sensitivity vs. specificity.
This feature too is highly experimental, so play with it at your own risk. And stay tuned, because we've already got some ideas on how to improve it further.
Variant recalibration is one of the most challenging parts of the Best Practices workflow, and not just for users! We've been wrestling with some of its internal machinery to produce better, more consistent modeling results, especially with call sets that are on the lower end of the size scale.
One of the breakthroughs we made was separating the parameters for the positive and negative training models. You know (or should know) that the VariantRecalibrator builds two separate models: one to model what "good" variants (i.e. true positives) look like (the positive model), and one to model what "bad" variants (i.e. false positives) look like (the negative model). Until now, we applied parameters the same way to both, but we've now realized that it makes more sense to treat them differently.
Because of how relative amounts of good and bad variants tend to scale differently with call set size, we also realized it was a bad idea to have the selection of bad variants be based on a percentage (as it has been until now) and instead switched it to a hard number. You can change this setting with the
--numBadVariants argument, which replaces the now-deprecated
Finally, we also found that the order of annotations matters. Now, instead of applying the annotation dimensions to the training model in the order that they were specified at the command line, VariantRecalibrator first reorders them based on their standard deviation. This stabilizes the training model and produces much more consistent results.
Some of you have been clamoring for more flexibility in handling individual BAM files and samples without losing the convenience of processing them in batches. In response, we've added the following:
For general GATK use, the
-sample_rename_mapping_file engine argument allows you to rename samples on-the-fly at runtime. It takes a file that maps bam files to sample names. Note that this does require that your BAM files contain single samples only, although multiple read groups are allowed.
For variant calling, the
-onlyEmitSamples argument allows you to tell the UnifiedGenotyper to only emit calls for specific samples among a cohort that you're calling in multisample mode, without emitting the calls for the rest of the cohort. Keep in mind however that the calculations will still be made on the entire cohort, and the annotation values emitted for those calls will reflect that.
For VQSR, the
--excludeFiltered flag tells the ApplyRecalibration tool not to emit sites that are filtered out by recalibration (i.e. do not write them to file).
And some of you went ahead and added the features you wanted yourselves!
Yossi Farjoun contributed a patch to enable allele-biased downsampling with different per-sample values for the HaplotypeCaller, emulating the equivalent functionality that was already available in the UnifiedGenotyper.
Louis Bergelson contributed a new read filter, LibraryReadFilter, which allows you to use only reads from a specific library in your analysis. This is the opposite (and somewhat more specific) functionality compared to the existing engine argument, --read_group_black_list , which allows you to exclude read groups based on specific tags (including but not limited to LB).
We have a new diagnostic tool, QualifyMissingIntervals, that allows you to collect metrics such as GC content, mapping quality etc. for a list of intervals of interest. This is something you'd typically want to use if you found (through other tools) that you're missing calls in certain intervals, and you want to find out what's going wrong in those regions.
Finally, those of you who have access to more sophisticated computing platforms, heads up! Version 2.7 comes with a version of the PairHMM algorithm (aka the bit that takes forever to run in HaplotypeCaller) that is optimized for running on FPGA chips. Credit goes to the fine folks at Convey Computer and Green Mountain Computing Systems who teamed up to develop this optimized version of the PairHMM, with a little help from our very own Tech Dev team. We're told further optimizations may be in store; in the meantime, they're seeing up to 300-fold speedups of HaplotypeCaller runs on Convey's platform. Not bad!
It's finally summer here in New England -- time for cave-dwelling developers to hit the beach and do the lobster dance (those of us who don't tan well anyway). We leave you with a new version of the GATK that includes a new(ish) plotting tool, some more performance improvements to the callers, a lot of feature tweaks and quite a few bug fixes. Be sure to check out the full list in the 2.6 Release Notes.
Highlights are below as usual, enjoy. There's one thing that we need to point out with particular emphasis: we have moved to Java 7, so you may need to update your system's Java version. Full explanation at the end of this document because it's a little long, but be sure to read it.
GATK old-timers may remember a tool called AnalyzeCovariates, which was part of the BQSR process in 1.x versions, many moons ago. Well, we've resurrected it to take over the plotting functionality of the BaseRecalibrator, to make it easier and faster to plot and compare the results of base recalibration. This also prevents issues with plot generation in scatter-gather mode. We'll update our docs on the BQSR workflow in the next few days, but in the meantime you can find full details of how to use this tool here.
We know you don't want to miss a single true variant, so for this release, we've put a lot of effort into making the HaplotypeCaller more sensitive. And it's paying off: in our tests, the HaplotypeCaller is now more sensitive than the UnifiedGenotyper for calling both SNPs and indels when run over whole genome datasets.
[graph to illustrate, coming soon]
You might think all our focus is on improving the HaplotypeCaller these days; you would be wrong. The UnifiedGenotyper is still essential for calling large numbers of samples together, for dealing with exotic ploidies, and for calling pooled samples. So we've given it a turbo boost that makes it go twice as fast for calling indels on multiple samples.
The key change here is the updated Hidden Markov Model used by the UG. You can see on the graph that as the number of exomes being called jointly increases, the new HMM keeps runtimes down significantly compared to the old HMM.
Don’t you hate it when you go back to a VCF you generated some months ago, and you have no idea which version of GATK you used at the time? (And yes, versions matter. Sometimes a lot.) We sure do, so we added a function to add the GATK version number in the header of the VCFs generated by GATK.
Speaking of software versions... As you probably know, the GATK runs on Java -- specifically, until now, version 6 of the Runtime Environment (which translates to version 1.6 if you ask
java -version at the command prompt). But the Java language has been evolving under our feet; version 7 has been out and stable for some time now, and version 8 is on the horizon. We were happy as clams with Java 6… but now, newer computers with recent OS versions ship with Java 7, and on MacOS X once you update the system it is difficult to go back to using Java 6. And since Java 7 is not fully backwards compatible, people have been running into version problems.
So, we have made the difficult but necessary decision to follow the tide, and migrate the GATK to Java 7. Starting with this release, GATK will now require Java 7 to run. If you try to run with Java 6, you will probably get an error like this:
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0
If you're not sure what version of Java you are currently using, you can find out very easily by typing the following command:
which should return something like this:
java version "1.7.0_17" Java(TM) SE Runtime Environment (build 1.7.0_17-b02) Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode)
If not, you'll need to update your java version. If you have any difficulty doing this, please don’t ask us in the forum -- you’ll get much better, faster help if you ask your local IT department.
This is going to be a short one, folks. The 2.5 release is pretty much all about bug fixes, with a couple of exceptions that we'll cover below.
Remember how we said that version 2.4 was going to be the least buggy ever? Well, that might have been a bit optimistic. We had a couple of stumpers in there -- and a flurry of little ones that were probably not novel (i.e. not specific to version 2.5) but finally bubbled up to the surface. We're not going to go over the bug fixes in detail, since the release notes include a comprehensive list. Basically, those are all fixed.
Well, not exactly new features, but noteworthy improvements to existing tools.
In addition to countless bug fixes, we've made drastic improvements to ReduceReads' compression algorithm, so you can now achieve much better compression rates without compromising on the retention of informative data. Keep in mind of course that as always, you'll see much bigger gains on certain types of data sets -- the higher the coverage in your original BAM files, the bigger the savings in file size and performance of the downstream tools.
We say this every time, and every time it's true: we've made some more improvements to the HaplotypeCaller that make it faster and more accurate. Well, it's still slower than the UnifiedGenotyper, in case you were going to ask (of course you were). But on the accuracy front, we say this without reservation or caveat: HC is now just as accurate as the UG for calling SNPs, and it is in a league of its own for calling indels. If you are even remotely interested in indels you should absolutely take it out for a spin. Go. Now.
Say goodbye to the mood swings and the pimples; it looks like this tool's awkward teenager phase is finally over. We've entirely reworked how DiagnoseTargets functions so it now uses a plugin system, which we think is much more convenient. This plugin system will be explained in detail in a forthcoming documentation article.
You may be aware that we had imposed a freeze of sorts on the annotation database version that could be used with the snpEff annotation. Well, we're happy to report that the author of the snpEff software package has made some significant upgrades, including a feature called GATK compatibility mode. As a result there is no longer any version constraint. We'll be updating our documentation on using snpEff with GATK soon (-ish), but in the meantime, feel free to go forth and annotate away. Just make sure to consult the snpEff manual for relevant information on using it with GATK.
Even as the dev team giveth, the dev team taketh away.
A few annotations were removed from the VariantAnnotator stables (as listed in the release notes), mainly because they didn't work properly. With all the caveats about how GATK is research software, we're still committed to providing quality tools that do something close to what they're advertised to do, at the bare minimum. If something doesn't fulfill that requirement, it's out.
We've also disabled the auto-generation of fai/dict files for fasta references. I can hear some of you groaning all the way from here. Yes, it was convenient -- but far too buggy. Come on people, it's a one-liner using Picard. Oh, and we're no longer allowing the use of compressed (.gz) references either -- also too buggy. The space savings were simply not worth the headaches.
Note: There are no version highlights available for versions earlier than 2.2.
GATK 3.4 was released on May 15, 2015. Itemized changes are listed below. For more details, see the user-friendly version highlights to be published soon.
Note that the release is in progress at time of posting -- it may take a couple of hours before the new GATK jar file is updated on the downloads page.
--mergeVariantsViaLDargument in HaplotypeCaller since it didn’t work. To merge complex substitutions, use ReadBackedPhasing as a post-processing step.
allowNonUniqueKmersInRefso that it applies to all kmer sizes. This resolves some assembly issues in low-complexity sequence contexts and improves calling sensitivity in those regions.
.g.vcffile extension. See Highlights for more details.
-uniquifySamplesto GenotypeGVCFs to make it possible to genotype together two different datasets containing the same sample.
-dcovsetting for HaplotypeCaller (pending a fix to the downsampling control system) to prevent buggy behavior. See Highlights for more details.
--breakBandsAtMultiplesOf Nwill ensure that no reference blocks span across genomic positions that are multiples of N. This is especially important in the case of scatter-gather where you don't want your scatter intervals to start in the middle of blocks (because of a limitation in the way
-Lworks in the GATK for VCF records with the END tag). See Highlights for more details.
-trimargument to trim (simplify) alleles to a minimal representation.
-trimAlternatesargument to remove all unused alternate alleles from variants. Note that this is pretty aggressive for monomorphic sites.
-noTrimargument to preserve original alleles.
-fixNDNflag fully functional.
-SMAis specified. Note that FORMAT fields behave the same as INFO fields - if the annotation has a count of A (one entry per Alt Allele), it is split across the multiple output lines. Otherwise, the entire list is output with each field.
-drfargument to disable default read filters. Limited to specific tools and specific filters (currently only DuplicateReadFilter).
-qsub-broadargument. When -qsub-broad is specified instead of
-qsub, Queue will use the
h_vmemparameter instead of
h_rssto specify memory limit requests. This was done to accommodate changes to the Broad’s internal job scheduler. Also causes the GridEngine native arguments to be output by default to the logger, instead of only when in debug mode.
slf4j-log4j12version (contributed by user Biocyberman).
GATK 3.3 was released on October 23, 2014. Itemized changes are listed below. For more details, see the user-friendly version highlights.
--sample_nameargument. This is a shortcut for people who have multi-sample BAMs but would like to use
-ERC GVCFmode with a particular one of those samples.
--ignore_all_filtersoption. If specified, the variant recalibrator will ignore all input filters and treat sites as unfiltered.
--keepOriginalAC functionalityin SelectVariants to work for sites that lose alleles in the selection.
read_grouparguments no longer appear in the header.
--bcffor VCF files, and
--generate_md5for BAM files moved to the engine level.
GATK 3.2 was released on July 14, 2014. Itemized changes are listed below. For more details, see the user-friendly version highlights.
We also want to take this opportunity to thank super-user Phillip Dexheimer for all of his excellent contributions to the codebase, especially for this release.
optfunctions to work with recent versions of the ggplot2 R library.
optfunctions to work with recent versions of the ggplot2 R library.
GATK 3.1 was released on March 18, 2014. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
--pair_hmm_implementation VECTOR_LOGLESS_CACHING. Please see the 3.1 Version Highlights for more details about expected speed ups and some background on the collaboration that made these possible.
GATK 3.0 was released on March 5, 2014. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
One important change for those who prefer to build from source is that we now use maven instead of ant. See the relevant documentation for building the GATK with our new build system.
GATK 2.8 was released on December 6, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Note that this release is relatively smaller than previous ones. We are working hard on some new tools and frameworks that we are hoping to make available to everyone for our next release.
GATK 2.7 was released on August 21, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
GATK 2.6 was released on June 20, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Important note: with this release the GATK has officially moved to using Java 7.
GATK 2.5 was released on April 30, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations
GATK release 2.2 was released on October 31, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Note: There are no release notes available for versions earlier than 2.0.
|1st May 2015||Update pom versions for the 3.4 release|
|1st May 2015||Merge remote-tracking branch 'unstable/master'|
|1st May 2015||Merge pull request #979 from broadinstitute/ami-fixASE-bug|
|1st May 2015||Merge pull request #978 from broadinstitute/dr_rev_htsjdk_and_picard|
|1st May 2015||Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central|
|1st May 2015||Merge pull request #947 from broadinstitute/rhl_invert_selection|
|1st May 2015||Merge pull request #981 from broadinstitute/eb_no_lone_dels|
|1st May 2015||Fixed a small feature/bug that I introduced with the spanning deletions genotyping.|
|1st May 2015||solve bug - now work also when the reads does not have mate|
|1st May 2015||Added invert and exclude flags for variant selection queries|
|1st May 2015||Merge pull request #974 from broadinstitute/jw_Var2BinPEDSwap|
|1st May 2015||Merge pull request #938 from broadinstitute/eb_fix_spanning_deletions_in_genotyping|
|1st May 2015||Correct errant array element swap in FAM file output.|
|1st May 2015||Added a fix for combining/genotyping positions over spanning deletions.|
|1st May 2015||Merge pull request #948 from broadinstitute/jw_deprecate_merge_var|
|30th April 2015||Deprecate --mergeVariantsViaLD in HC|
|30th April 2015||Merge pull request #968 from broadinstitute/gg_unexclude_annotations_#966|
|30th April 2015||Moved MQ0 out of HC exclusion and into StandardUGAnnotation|
|30th April 2015||Un-exclude SD and TRA from HC annotators; resolves #966|
|30th April 2015||Merge pull request #970 from broadinstitute/gg_minor_docfixes|
Note: There are no PDF files of the Guide Book available for versions earlier than 2.3-9.