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Reference genome

Last update: 20230727

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Reference genome datasets are prepared and stored at:

  • /project/data/shared
    • Read-only
    • Datamanager control
    • Includes: README.md
    • Includes: ref.sh creation

GRCh38

Choice

Reference genome choice is discussed succinctly in many difference places. Therefore, we link other usefull sources.

  • Heng Li - Which human reference genome to use?

https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

  • Illumina review

https://www.illumina.com/science/genomics-research/articles/dragen-demystifying-reference-genomes.html

Our reference genome was donwloaded and installed by ref.sh which does the following:

Installation

  • Get local copy
    wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz`
  • Get checksum
    md5 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz > GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz.md5
  • Transfer to cluster
    sftp username@cluster
cd data/ref
put GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
put GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz.md5
put ref.sh
  • Preparation
  • Once downloaded we need the index which is done by
    bwa index GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

Other builds

We use GRCh38 but for some old prepared data we must use the existing version with the reference genome used at that time. The mentioned refernce is “human_g1k_v37_decoy_chr.fasta”. There are 4 common “hg19” references, and they are NOT directly interchangeable: https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies