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GATK Bundle

Stephen J Newhouse edited this page Feb 5, 2017 · 3 revisions

GATK Bundle

Feb 2017

Data at: ftp://gsapubftp-anonymous@ftp.broadinstitute.org

Quick dirty way of getting some data e.g ucsc.hg19.fasta from bundle/hg19:-

wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/ucsc.hg19.fasta.gz

b38

In progress...

/bundle/hg38/1000G_omni2.5.hg38.vcf.gz
/bundle/hg38/1000G_omni2.5.hg38.vcf.gz.tbi
/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz
/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
/bundle/hg38/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz
/bundle/hg38/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi
/bundle/hg38/beta
/bundle/hg38/beta/Homo_sapiens_assembly38.dbsnp.vcf.gz
/bundle/hg38/beta/Homo_sapiens_assembly38.dbsnp.vcf.gz.tbi
/bundle/hg38/beta/Homo_sapiens_assembly38.dbsnp138.vcf.gz
/bundle/hg38/beta/Homo_sapiens_assembly38.known_indels.vcf.gz
/bundle/hg38/beta/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
/bundle/hg38/beta/Homo_sapiens_assembly38.variantEvalGoldStandard.vcf.gz
/bundle/hg38/beta/Homo_sapiens_assembly38.variantEvalGoldStandard.vcf.gz.tbi
/bundle/hg38/beta/NISTIntegratedCalls.hg38.interval_list
/bundle/hg38/beta/NISTIntegratedCalls.hg38.vcf.gz
/bundle/hg38/beta/NISTIntegratedCalls.hg38.vcf.gz.tbi
/bundle/hg38/beta/wholegenome.interval_list
/bundle/hg38/dbsnp_138.hg38.vcf.gz
/bundle/hg38/dbsnp_138.hg38.vcf.gz.tbi
/bundle/hg38/dbsnp_144.hg38.vcf.gz
/bundle/hg38/dbsnp_144.hg38.vcf.gz.tbi
/bundle/hg38/dbsnp_146.hg38.vcf.gz
/bundle/hg38/dbsnp_146.hg38.vcf.gz.tbi
/bundle/hg38/hapmap_3.3.hg38.vcf.gz
/bundle/hg38/hapmap_3.3.hg38.vcf.gz.tbi
/bundle/hg38/Homo_sapiens_assembly38.dict
/bundle/hg38/Homo_sapiens_assembly38.fasta.64.alt
/bundle/hg38/Homo_sapiens_assembly38.fasta.fai
/bundle/hg38/Homo_sapiens_assembly38.fasta.gz
/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
/bundle/hg38/wgs_calling_regions.hg38.interval_list

hg19

/bundle/hg19/1000G_omni2.5.hg19.sites.vcf.gz
/bundle/hg19/1000G_omni2.5.hg19.sites.vcf.gz.md5
/bundle/hg19/1000G_omni2.5.hg19.sites.vcf.idx.gz
/bundle/hg19/1000G_omni2.5.hg19.sites.vcf.idx.gz.md5
/bundle/hg19/1000G_phase1.indels.hg19.sites.vcf.gz
/bundle/hg19/1000G_phase1.indels.hg19.sites.vcf.gz.md5
/bundle/hg19/1000G_phase1.indels.hg19.sites.vcf.idx.gz
/bundle/hg19/1000G_phase1.indels.hg19.sites.vcf.idx.gz.md5
/bundle/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz
/bundle/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz.md5
/bundle/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.idx.gz
/bundle/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.idx.gz.md5
/bundle/hg19/CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.gz
/bundle/hg19/CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.gz.md5
/bundle/hg19/CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.idx.gz
/bundle/hg19/CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.idx.gz.md5
/bundle/hg19/dbsnp_138.hg19.excluding_sites_after_129.vcf.gz
/bundle/hg19/dbsnp_138.hg19.excluding_sites_after_129.vcf.gz.md5
/bundle/hg19/dbsnp_138.hg19.excluding_sites_after_129.vcf.idx.gz
/bundle/hg19/dbsnp_138.hg19.excluding_sites_after_129.vcf.idx.gz.md5
/bundle/hg19/dbsnp_138.hg19.vcf.gz
/bundle/hg19/dbsnp_138.hg19.vcf.gz.md5
/bundle/hg19/dbsnp_138.hg19.vcf.idx.gz
/bundle/hg19/dbsnp_138.hg19.vcf.idx.gz.md5
/bundle/hg19/hapmap_3.3.hg19.sites.vcf.gz
/bundle/hg19/hapmap_3.3.hg19.sites.vcf.gz.md5
/bundle/hg19/hapmap_3.3.hg19.sites.vcf.idx.gz
/bundle/hg19/hapmap_3.3.hg19.sites.vcf.idx.gz.md5
/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz
/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz.md5
/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx.gz
/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx.gz.md5
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf.gz
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf.gz.md5
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf.idx.gz
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf.idx.gz.md5
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.gz
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.gz.md5
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.idx.gz
/bundle/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.idx.gz.md5
/bundle/hg19/NA12878.knowledgebase.snapshot.20131119.hg19.vcf.gz
/bundle/hg19/NA12878.knowledgebase.snapshot.20131119.hg19.vcf.gz.md5
/bundle/hg19/NA12878.knowledgebase.snapshot.20131119.hg19.vcf.idx.gz
/bundle/hg19/NA12878.knowledgebase.snapshot.20131119.hg19.vcf.idx.gz.md5
/bundle/hg19/ucsc.hg19.dict.gz
/bundle/hg19/ucsc.hg19.dict.gz.md5
/bundle/hg19/ucsc.hg19.fasta.fai.gz
/bundle/hg19/ucsc.hg19.fasta.fai.gz.md5
/bundle/hg19/ucsc.hg19.fasta.gz
/bundle/hg19/ucsc.hg19.fasta.gz.md5

b37

/bundle/b37/1000G_omni2.5.b37.vcf.gz
/bundle/b37/1000G_omni2.5.b37.vcf.gz.md5
/bundle/b37/1000G_omni2.5.b37.vcf.idx.gz
/bundle/b37/1000G_omni2.5.b37.vcf.idx.gz.md5
/bundle/b37/1000G_phase1.indels.b37.vcf.gz
/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5
/bundle/b37/1000G_phase1.indels.b37.vcf.idx.gz
/bundle/b37/1000G_phase1.indels.b37.vcf.idx.gz.md5
/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz
/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5
/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx.gz
/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.idx.gz.md5
/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz
/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz.tbi
/bundle/b37/Broad.human.exome.b37.interval_list.gz
/bundle/b37/Broad.human.exome.b37.interval_list.gz.md5
/bundle/b37/CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf.gz
/bundle/b37/CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf.gz.md5
/bundle/b37/CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf.idx.gz
/bundle/b37/CEUTrio.HiSeq.WGS.b37.bestPractices.b37.vcf.idx.gz.md5
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.bam
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.bam.bai.gz
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.bam.bai.gz.md5
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.bam.md5
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.vcf.gz
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.vcf.gz.md5
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.vcf.idx.gz
/bundle/b37/CEUTrio.HiSeq.WGS.b37.NA12878.vcf.idx.gz.md5
/bundle/b37/dbsnp_138.b37.excluding_sites_after_129.vcf.gz
/bundle/b37/dbsnp_138.b37.excluding_sites_after_129.vcf.gz.md5
/bundle/b37/dbsnp_138.b37.excluding_sites_after_129.vcf.idx.gz
/bundle/b37/dbsnp_138.b37.excluding_sites_after_129.vcf.idx.gz.md5
/bundle/b37/dbsnp_138.b37.vcf.gz
/bundle/b37/dbsnp_138.b37.vcf.gz.md5
/bundle/b37/dbsnp_138.b37.vcf.idx.gz
/bundle/b37/dbsnp_138.b37.vcf.idx.gz.md5
/bundle/b37/hapmap_3.3.b37.vcf.gz
/bundle/b37/hapmap_3.3.b37.vcf.gz.md5
/bundle/b37/hapmap_3.3.b37.vcf.idx.gz
/bundle/b37/hapmap_3.3.b37.vcf.idx.gz.md5
/bundle/b37/human_g1k_v37_decoy.dict.gz
/bundle/b37/human_g1k_v37_decoy.dict.gz.md5
/bundle/b37/human_g1k_v37_decoy.fasta.fai.gz
/bundle/b37/human_g1k_v37_decoy.fasta.fai.gz.md5
/bundle/b37/human_g1k_v37_decoy.fasta.gz
/bundle/b37/human_g1k_v37_decoy.fasta.gz.md5
/bundle/b37/human_g1k_v37.dict.gz
/bundle/b37/human_g1k_v37.dict.gz.md5
/bundle/b37/human_g1k_v37.fasta.fai.gz
/bundle/b37/human_g1k_v37.fasta.fai.gz.md5
/bundle/b37/human_g1k_v37.fasta.gz
/bundle/b37/human_g1k_v37.fasta.gz.md5
/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz.md5
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz.md5
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz.md5
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz
/bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz.md5
/bundle/b37/NA12878.knowledgebase.snapshot.20131119.b37.vcf.gz
/bundle/b37/NA12878.knowledgebase.snapshot.20131119.b37.vcf.gz.md5
/bundle/b37/NA12878.knowledgebase.snapshot.20131119.b37.vcf.idx.gz
/bundle/b37/NA12878.knowledgebase.snapshot.20131119.b37.vcf.idx.gz.md5

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