NOTE: we are currently working on overhauling the bundle to 1) add support for Hg38 and 2) document the provenance of the resource files more fully.
1. Obtaining the bundle
We provide these files (or corresponding .gz versions) from the GSA FTP Server in the directory called bundle. Note that there is no "current link" on the FTP; users should download the highest numbered directory under current (this is the most recent data set).
If you have access to the Broad VPN (Broadies and collaborators only), the latest bundle will always be available in:
/humgen/gsa-hpprojects/GATK/bundle/current
with a subdirectory containing for each reference sequence and associated data files.
2. b37 Resources: the Standard Data Set
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)
- Mills_and_1000G_gold_standard.indels.b37.sites.vcf
The latest set from 1000G phase 3 (v4) for genotype refinement: 1000G_phase3_v4_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 Note that this resource is out of date and does not represent the results of our Best Practices.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.
3. 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.
4. b36 Resources: lifted over from b37
Includes the 1000 Genomes pilot b36 formated reference sequence (human_b36_both.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.
5. hg19 Resources: lifted over from b37
Includes the UCSC-style hg19 reference along with all lifted over VCF files.