GRCh38 (hg38) reference bundle with pre-built BWA and minimap2 indexes

A ready-to-use GRCh38 reference bundle for short-read alignment and variant-calling pipelines, packaged to avoid the time and memory cost of rebuilding indexes from scratch.

Contents:

  - hg38.fa: uncompressed reference FASTA  - hg38.fa.fai: samtools index  - hg38.dict: sequence dictionary (Picard/GATK)  - hg38.fa.{amb,ann,bwt,pac,sa}: BWA-MEM index  - hg38.asm5.mmi: minimap2 asm5 preset index (suitable for assembly-to-reference alignment, e.g. dipcall)  - hg38.sdf/: RTG Sequence Data Format directory (required by rtg vcfeval)

  Source: hg38.fa.gz from the UCSC Genome Browser (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/), decompressed.  Sequences are unmodified, including primary chromosomes (chr1 to 22, chrX, chrY, chrM), unplaced/unlocalized contigs, and ALT contigs.

  # Place all four downloads in the same directory, then:                                                                       tar -xzf hg38_fa.tar.gz     # -> hg38.fa, hg38.fa.fai, hg38.dict                                                              tar -xf  hg38_bwa.tar       # -> hg38.fa.{amb,ann,bwt,pac,sa}                                                                 tar -xf  hg38_sdf.tar       # -> hg38.sdf/                                                                                    # hg38.asm5.mmi is already usable as-is                                                                                                                                                                                                                     # Optional cleanup                                                                                                            rm hg38_fa.tar.gz hg38_bwa.tar hg38_sdf.tar