Resource bundle

IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here

created by GATK_Team

on 2017-12-24

The GATK resource bundle is a collection of standard files for working with human sequencing data. We provide several versions of the bundle corresponding to the various reference builds, but be aware that we no longer support very old versions (b36/hg18). In addition, we are currently transitioning to support the Grch38/hg38 reference build, which will eventually become the default, while b37/hg19 will be considered legacy and eventually phased out. See the Dictionary entry on human genome reference builds for more information.

We do not currently provide any non-human resources in the resource bundle.

1. Accessing the bundle

See the Resource Bundle page. In a nutshell, there's a Google Cloud bucket and an FTP server. These resources are also available through FireCloud, our cloud-based analysis portal, in workspaces that are preconfigured for the major Best Practices analysis use cases.

2. Grch38/Hg38 Resources: the soon-to-be Standard Set

This contains all the resource files needed for Best Practices germline short variant discovery in whole-genome sequencing data (WGS). Exome files and itemized resource list coming soon(ish). Somatic resources are in development.

3. b37 Resources: the Standard Data Set pending completion of the Hg38 bundle

Note that many of these resources are out of date and will eventually be retired. All new development is being done against Grch38/hg38.

• Reference sequence (standard 1000 Genomes fasta) along with fai and dict files
• dbSNP in VCF. This includes two files:
  • A recent dbSNP release (build 138)
  • This file subsetted to only sites discovered in or before dbSNPBuildID 129, which excludes the impact of the 1000 Genomes project and is useful for evaluation of dbSNP rate and Ti/Tv values at novel sites.
• HapMap genotypes and sites VCFs
• OMNI 2.5 genotypes for 1000 Genomes samples, as well as sites, VCF
• The current best set of known indels to be used for local realignment (note that we don't use dbSNP for this anymore); use both files:
  • 1000G_phase1.indels.b37.vcf (currently from the 1000 Genomes Phase I indel calls)
  • Millsand1000Ggoldstandard.indels.b37.sites.vcf
• The latest set from 1000G phase 3 (v4) for genotype refinement: 1000Gphase3v4_20130502.sites.vcf
• A large-scale standard single sample BAM file for testing:
  • NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam containing ~64x reads of NA12878 on chromosome 20
  • A callset produced by running UnifiedGenotyper on the dataset above. Note that this resource is out of date and does not represent the results of our Best Practices. This will be updated in the near future.
• The Broad's custom exome targets list: Broad.human.exome.b37.interval_list (note that you should always use the exome targets list that is appropriate for your data, which typically depends on the prep kit that was used, and should be available from the kit manufacturer's website)

Additionally, these files all have supplementary indices, statistics, and other QC data available.

All resources below this are available only on the FTP server, not on the cloud.

4. hg19 Resources: lifted over from b37

Includes the UCSC-style hg19 reference along with all lifted over VCF files.

5. hg18 Resources: lifted over from b37

Includes the UCSC-style hg18 reference along with all lifted over VCF files. The refGene track and BAM files are not available. We only provide data files for this genome-build that can be lifted over "easily" from our master b37 repository. Sorry for whatever inconvenience that this might cause.

Also includes a chain file to lift over to b37.

6. b36 Resources: lifted over from b37

Includes the 1000 Genomes pilot b36 formatted reference sequence (humanb36both.fasta) along with all lifted over VCF files. The refGene track and BAM files are not available. We only provide data files for this genome-build that can be lifted over "easily" from our master b37 repository. Sorry for whatever inconvenience that this might cause.

Also includes a chain file to lift over to b37.

From Bekir on 2018-09-10

Hello,

There was a problem with the file “1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf” which prevented me using it for annotation for chromosomes chr16-chr22. Lengths of chr16 and chr17 look the same in the header:

> contig=

> contig=

I am guessing that positions of chr16-chr22 were all shifted due to a concatenation issue. Can you please fix this issue?

Best, Bekir

From oneillkza on 2018-11-26

As I discovered, the hg19 resources actually are available on the cloud:

https://console.cloud.google.com/storage/browser/gatk-legacy-bundles/b37

From pwaltman on 2018-11-27

> @oneillkza said:

> As I discovered, the hg19 resources actually are available on the cloud:

>

> https://console.cloud.google.com/storage/browser/gatk-legacy-bundles/b37

Nice catch!! Wish I saw this before I spent multiple hours downloading this from the ftp site last night, but hopefully someone else will see it!