GRCh38 and BWA indices used can be downloaded from the pre-computed 1000 genomes GRCh38 BWA database at ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/ (with decoys). We also have made them available via this repository.
- GRCh38 full analysis set plus decoy hla
- GRCh38 full analysis set plus decoy hla.alt
- GRCh38 full analysis set plus decoy hla.amb
- GRCh38 full analysis set plus decoy hla.ann
- GRCh38 full analysis set plus decoy hla.bwt
- GRCh38 full analysis set plus decoy hla.fai
- GRCh38 full analysis set plus decoy hla.pac
- GRCh38 full analysis set plus decoy hla.sa
- SIRVome isoforms ERCCs 170612a.fasta
- SIRVome isoforms ERCCs Lot001485 C 170612a.gtf
- SIRVome isoforms ERCCs Lot001485 I 170612a.gtf
- SIRVome isoforms ERCCs Lot001485 O 170612a.gtf
GENCODE v27 files can be found at https://www.gencodegenes.org/human/release_27.html.