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Reference archives

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Keiran Raine edited this page May 7, 2019 · 7 revisions

We support a limited number of pre-constructed reference sets.

Pre-generated reference sets

Human GRCh37

Core reference files for fragment based analysis (2.x +):

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/core_ref_GRCh37d5.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/VAGrENT_ref_GRCh37d5_ensembl_75.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/SNV_INDEL_ref_GRCh37d5-fragment.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/CNV_SV_ref_GRCh37d5_brass6+.tar.gz

SNV/INDEL pre 2.x:

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/SNV_INDEL_ref_GRCh37d5.tar.gz

If you are using pre 2.1.x releases you need the subclonal calling reference set to support cgpBattenberg. If not needed you can omit this by specifying -skipbb:

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/SUBCL_ref_GRCh37d5.tar.gz

Human GRCh38

Please use version 2.1.0+ releases when processing GRCh38. The "current" version of reference files can be found here:

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/bwa_idx_GRCh38_hla_decoy_ebv.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/core_ref_GRCh38_hla_decoy_ebv.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/qcGenotype_GRCh38_hla_decoy_ebv.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz

All releases of reference file are stored in a YYYYMM folder, if you want consistent execution and further details please see the README:

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/README.md

Generating alternative reference sets

You are able to build your own reference bundles for different species and naming conventions. You need to construct archives emulating those above (the first element of the path within the archive is dropped in all cases).

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