1. Reference files

dockstore-cgpmap requires a core reference file (genome.fa) and it's corresponding index files (genome.fa.alt, genome.fa.amb, genome.fa.ann, genome.fa.bwt, genome.fa.bwt.2bit.64, genome.fa.pac, genome.fa.sa).

If you are planning to run dockstore-cgpmap with Bwa-mem2, you will also need the additional reference files genome.fa.bwt.2bit.64 and genome.fa.0123.

The Sanger Institute supplies full pre-generated references sets for mapping to GRCh37 and GRCh38. To run with Bwa-mem2, download the alternative index archive with the _bwamem2 suffix.

GRCh37

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/core_ref_GRCh37d5.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/bwa_idx_GRCh37d5.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/bwa_idx_GRCh37d5_bwamem2.tar.gz

GRCh38

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/bwa_idx_GRCh38_hla_decoy_ebv.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/bwa_idx_GRCh38_hla_decoy_ebv_bwamem2.tar.gz