HOWTO

Building indexes

Depend on your purpose, you have to download reference sequence, gene annotation and SNP files.
We also provides scripts to build indexes. Download

Prepare data

  1. Download reference 
    $ wget ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
$ gzip -d Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
$ mv Homo_sapiens.GRCh38.dna.primary_assembly.fa genome.fa
  2. Download GTF and make exon, splicesite file.
    If you want to build HFM index, you can skip this step. 
    $ wget ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz  
$ gzip -d Homo_sapiens.GRCh38.84.gtf.gz
$ mv Homo_sapiens.GRCh38.84.gtf genome.gtf
$ hisat2_extract_splice_sites.py genome.gtf > genome.ss
$ hisat2_extract_exons.py genome.gtf > genome.exon
  3. Download SNP
    If you want to build HFM index, you can skip this step. 
    $ wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/snp144Common.txt.gz
$ gzip -d snp144Common.txt.gz

    Convert chromosome names of UCSC Database to Ensembl Annotation

    $ awk 'BEGIN{OFS="\t"} {if($2 ~ /^chr/) {$2 = substr($2, 4)}; if($2 == "M") {$2 = "MT"} print}' snp144Common.txt > snp144Common.txt.ensembl

    make SNPs and haplotype file

    $ hisat2_extract_snps_haplotypes_UCSC.py genome.fa snp144Common.txt.ensembl genome

Build HFM index

It takes about 20 minutes(depend on HW spec) to build index, and requires at least 6GB memory.

$ hisat2-build -p 16 genome.fa genome

Build HGFM index with SNPs

$ hisat2-build -p 16 --snp genome.snp --haplotype genome.haplotype genome.fa genome_snp

Build HGFM index with transcripts

It takes about 1 hour(depend on HW spec) to build index, and requires at least 160GB memory.

$ hisat2-build -p 16 --exon genome.exon --ss genome.ss genome.fa genome_tran

Build HGFM index with SNPs and transcripts

$ hisat2-build -p 16 --snp genome.snp --haplotype genome.haplotype --exon genome.exon --ss genome.ss genome.fa genome_snp_tran