GRCh38 mapping of the Illumina Platinum Genomes CEU pedigree

2015-10-16 00:00:00 +0100

We have aligned the Illumina Platinum pedigree sequence data to GRCh38. The data was aligned to the full assembly including the GRC maintained alternate loci along with decoy and additional HLA sequences from the IMGT. A copy of the FASTA file can be found in our reference directory. The alignment was carried out using a new alt-aware version of BWA-mem.

The alignment files themselves can be found in the data_collections/illumina_platinum_pedigree/data directory.

The alignment index and sequence index can be found in the data_collections/illumina_platinum_pedigree directory.

Please note, alignment files are now being distributed in CRAM format, rather than BAM format. You can find more details about CRAM in this README

Further details of our alignment pipeline can be found in the data collection README.

If you have any questions please email