Latest Release: 12/4/18
Release Notes can be found here.

TCGA Reference Files

jneffjneff BostonMember, Broadie, Moderator admin

The following FireCloud Reference Files reside in the FireCloud TCGA Open Access Bucket. These files are references in FireCloud's best practice workspaces, e.g., Broad_GISTIC2__Workflow_BestPractice. They will appear as workspace attributes within the workspace summary tab.

You can clone any of the best practice workspaces that reference these files. In this case, you will not be charged for storage because the file paths will still point to the FireCloud TCGA Open Access Bucket. You will, however, be responsible for any compute charges when you run an analysis within your cloned workspace.

Note that all of these files use the HG19 genome build. In the future, we may provide reference files for multiple genome builds, e.g., HG38.

HG19 Genome Build

<

table border="1" align="left">





File TypeFireCloud AttributeGoogle Bucket


INTERVALSWGS_INTERVALSHomo_sapiens_assembly19.fasta.wgs_intervals.interval_list


INTERVALSMUTECT_FC_INTERVALS<a href="gs://firecloud-tcga-open-access/tutorial/reference/panel_100_genes.interval_list>panel_100_genes.interval_list


INTERVALS SNP6BEDSNP6.hg19.interval_list


INTERVALS EXOME_INTERVALSplus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list


INTERVALS PICARD_BAIT_INTSHomo_sapiens_assembly19.baits.interval_list


INTERVALS PICARD_TGT_INTSHomo_sapiens_assembly19.targets.interval_list


TAR.GZONCO_TARGZ_HGREFjust_ref_hg.tar.gz


TAR.GZONCO_TARBALLJan262014.tar.gz


TARONCO_TARJan262014.tar


TARONCO_TAR_HGREFjust_ref_hg.tar


DB (ZIP)CAP_NORM_DB_ZIP hg19_v4.zip


TXTHAP_DB_FOR_CChaplotype_database.txt


TXTCYTO_BANDcytoBand.txt


TXTgenome_info probes_sorted_2.1.txt


REGIONSCapture_regions_listcapture_regions_list


GTFgenes_gtf model.patched_contigs.gtf


GTFtranscripts_gtftranscripts.patched_contigs.gtf


MAT refgene_filev18_20140127.mat


VCFCOSMIC_VCF hg19_cosmic_v54_120711.vcf


VCFHAP_MAP_VCFhapmap_3.3.fixed.vcf


VCFDB_SNP_VCF 134_b37.leftAligned.vcf


TXTcnv_fileCNV.hg19.bypos.111213.txt


TXTRG_BLread_group_blacklist.v1.txt


FASTA FA Homo_sapiens_assembly19.fasta


FASTA ReferenceFastahuman_g1k_v37_decoy.fasta /a>


FASTAgenome_fasta
Homo_sapiens_assembly19.fasta


DICTFA_DICTHomo_sapiens_assembly19.dict


DICTReferenceFastaDict human_g1k_v37_decoy.dict


FAIFA_IDXHomo_sapiens_assembly19.fasta.fai


FAIReferenceFastaIndexhuman_g1k_v37_decoy.fasta.fai


FAIgenome_fasta_indexHomo_sapiens_assembly19.fasta.fai


IDX DB_SNP_VCF_IDX dbsnp_134_b37.leftAligned.vcf.idx


BEDhg19.bed gaf_20111020+broad_wex_1.1_hg19.bed


BED recapseg_agilent_bedtargets_germline_copy_number_variants_X_Y_removed.bed


BEDtargets_bedHomo_sapiens_assembly19.targets.bed


TAR.GZrsem_referencersem_reference_v19.tar.gz


TAR.GZstar_indexstar_index_v19_oh75.tar.gz


TSVgood_hets only_very_good_hets.tsv


TXT markers_file minus_frequent_nan_probes_sorted_2.1.txt


MuTect PONKGENOMES_NORMAL_PANEL_VCF 10bp_hg19_300_1kg_normal_panel.vcf


Filter PONTOKENS_PONfinal_summed_tokens.hist.bin


CN PON open_access_gatk_cnv_ponopen_access_pon_from_1000g.pon


Mega PON Mega_PONMega_PoN_v2.6.pon

Please post a comment on this article if you have any questions.

Post edited by Geraldine_VdAuwera on
Sign In or Register to comment.