GRCh38.p13 Reference FASTA (bgzip'd with faidx)

This is derived from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz.

A short name (chr1, chr2, ... chr22, chrX, chrY, chrM) has been added to each primary chromosomal sequence.

It has then been recompressed with bgzip and indexed with samtools:

curl -#fSL https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz -o genomic.fna.gz
gunzip genomic.fna.gz
cat genomic.fna | sed -r 's/^>(NC.*Homo sapiens chromosome ([0-9XY]+),.*)/>chr\2 \1/g' | sed -r 's/^>(NC.*Homo sapiens mitochondrion,.*)/>chrM \1/g' > chrfix.fna
bgzip -c chrfix.fna > reference.fna.bgz
samtools faidx reference.fna.bgz
tar -czvf GRCh38_reference_fasta.tar reference.fna.bgz reference.fna.bgz.fai reference.fna.bgz.gzi

This tar file contains:

• reference.fna.bgz
• reference.fna.bgz.fai
• reference.fna.bgz.gzi