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Build GRCh38

The Genome Reference Consortium Human Build 38 (GRCh38), or hg38, serves as a standardized representation of DNA sequences for various alignment and analysis pipelines.

The specific version in use is GCA_000001405.15 no_alt_analysis_set, accessible for download here in the following files:

Sequences FASTA: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
FM Index: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bwa_index.tar.gz

This version excludes ALT contigs and Human decoy sequences from hs38d1 (GCA_000786075.2), and includes the following sequences:

Chromosomes from the GRCh38 Primary Assembly unit.
Mitochondrial genome from the GRCh38 non-nuclear assembly unit.
Unlocalized scaffolds from the GRCh38 Primary Assembly unit.
Unplaced scaffolds from the GRCh38 Primary Assembly unit.
Epstein-Barr virus (EBV) sequence.

Note: The two PAR regions on chrY have been hard-masked with Ns, and the chromosome Y sequence is not identical to the GenBank sequence but shares the same coordinates. Similarly, duplicate copies of centromeric arrays and WGS on chromosomes 5, 14, 19, 21 & 22 have been hard-masked with Ns.

Note: The EBV sequence is not part of the genome assembly but is included in the analysis set for aligning reads often present in sequencing samples.

Generating FASTA Index Files

Decompress the FNA file

gunzip GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

Change the file extension to `.fasta`

mv GCA_000001405.15_GRCh38_no_alt_analysis_set.fna GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta

Create the `faidx` index (requires samtools)

samtools faidx GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta

Create the sequence dictionary (requires picard)

java -jar picard.jar CreateSequenceDictionary R=GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta

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