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Configuration

The configuration file defines the values for the parameters below. Default values are described in workflow/schemas/config.schema.yaml. If the user provides a config file, it is validated against this schema.

  • organism: Takes human or mouse
  • release: Gencode release version (starts with M for mouse)
  • genome_build: Genome build version, has to match the release (currently supported: GRCh38, GRCm39, GRCm38)
  • gnomad_release: Version of the gnomad release (suggested version: 4.1)
  • intron_slop: Number of intronic bases that should extend the exome definition ref_exome.bed (suggested: 20)
  • exome_transcript_definition: Define which GENCODE transcripts should be used to create the exome definition. The default is the "basic" tag. Please note that GENCODE basic definitions were deprecated in version 48 and replaced by the tag "GENCODE_Primary". These are not the same sets of transcripts. For now, we recommend continuing to use basic transcripts.
  • star_sjdb_overhang: --sjdbOverhang parameter for STAR index generation (should be read length - 1, in most cases 100 should be sufficient)
  • star_genome_sa_index_n_bases: Defines the STAR parameter genomeSAindexNbases (default 14). The lower the value, the smaller the index. This can be useful, when creating test data for CI tests to keep the file small.
  • minimum_allele_frequency (only required in human mode): af_only_gnomad_hg38.vcf.gz variants are filtered for population allele frequency > this cutoff (suggested: 0.001)
  • gencode_url: URL of GENCODE, where reference genome and annotation is downloaded from (default: "https://ftp.ebi.ac.uk/pub/databases/gencode")
  • ucsc_url (only required in human mode): URL of UCSC FTP (default: "https://hgdownload.soe.ucsc.edu/gbdb/hg38")
  • ucsc_golden_path_url (only required in human mode): URL of UCSC golden path (default: "https://hgdownload.soe.ucsc.edu/goldenPath")
  • gatk_url (only required in human mode): URL of GATK resource bundle (default: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0")
  • gnomad_url (only required in human mode): URL of GNOMAD (default: "https://storage.googleapis.com/gcp-public-data--gnomad/release")
  • chrom_filter: List of chromosome names that should be contained in the af_only_gnomad_hg38.vcf.gz file

On top of that, we use the config/container_config.yaml file to specify URLs for the apptainer/docker containers --sdm apptainer.

Example Human

An example config file to create a human OBLX Library. Unless required, it is recommended to use the default configuration (see workflow/schemas/config.schema.yaml).

organism: human
release: "49"
genome_build: GRCh38
gnomad_release: 4.1

# adds the defined slop to the generic exome definition (+/- intron_slop bp of intronic sequence)
intron_slop: 20

# Parameter for STAR index creation. Adapt to the read size if necessary
star_sjdb_overhang: 100
star_genome_sa_index_n_bases: 14

# Remove variants from gnomad VCF with poplutation allele frequency <= this cutoff
minimum_allele_frequency: 0.001

gencode_url: "https://ftp.ebi.ac.uk/pub/databases/gencode"
ucsc_url: "https://hgdownload.soe.ucsc.edu/gbdb/hg38"
ucsc_golden_path_url: "https://hgdownload.soe.ucsc.edu/goldenPath"
gatk_url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0"
gnomad_url: "https://storage.googleapis.com/gcp-public-data--gnomad/release"

chrom_filter:
  - chr1
  - chr2
  - chr3
  - chr4
  - chr5
  - chr6
  - chr7
  - chr8
  - chr9
  - chr10
  - chr11
  - chr12
  - chr13
  - chr14
  - chr15
  - chr16
  - chr17
  - chr18
  - chr19
  - chr20
  - chr21
  - chr22
  - chrX
  - chrY

Example Mouse

An example config file for mouse mode:

organism: mouse
release: "M36"
genome_build: GRCm39

# adds the defined slop to the generic exome definition (+/- intron_slop bp of intronic sequence)
intron_slop: 20

# Parameter for STAR index creation. Adapt to the read size if necessary
star_sjdb_overhang: 100
star_genome_sa_index_n_bases: 14

Support for non-GENCODE organisms

OBLX also supports generation of libraries for organisms that are not available via GENCODE. Therefore the resources are pulled from Ensembl FTP. To use data from Ensembl, specify in the config file the following parameters:

  • organism: The Ensembl organism name (begin with capital letter and "_" separated, e.g. Rattus_norvegicus or Capra_hircus).
  • release: Specify the Ensembl release in quotation marks (e.g., "116").
  • genome_build: The genome build (e.g., "GRCr8", "GRCh38", ...).
  • chromosome_mapping_file: Path to a tab separated file mapping the Ensembl chromosome names to the UCSC chromosome naming convention. Note: This has to be provided as an absolute path (e.g. /path/to/your/chrom_mapping.txt).
  • exome_transcript_definition: Transcripts to filter for when generating the resources/exome_definition/ref_exome.bed file (default: basic).
  • ensembl_mysql_build: Build for the organism in the Ensembl mysql FTP (see https://ftp.ensembl.org/pub/release-116/mysql/; e.g., rattus_norvegicus_core_116_1/ would be "1").
  • chrom_filter: Chromosomes to download and filter VCF. You can check https://ftp.ensembl.org/pub/release-116/fasta/rattus_norvegicus/dna/ which chromosomes are available for the specified organism.
organism: Rattus_norvegicus
release: "116"
genome_build: GRCr8
chromosome_mapping_file: /path/to/your/chromosome/mapping/file/rat_map.txt
exome_transcript_definition: "gencode_basic"
ensembl_mysql_build: "1"
chrom_filter:
  - "1"
  - "2"
  - "3"
  - "4"
  - "5"
  - "6"
  - "7"
  - "8"
  - "9"
  - "10"
  - "11"
  - "12"
  - "13"
  - "14"
  - "15"
  - "16"
  - "17"
  - "18"
  - "19"
  - "20"
  - "MT"
  - "X"
  - "Y"

Example of the chromosome_mapping_file for the above config file:

1   chr1
10  chr10
11  chr11
12  chr12
13  chr13
14  chr14
15  chr15
16  chr16
17  chr17
18  chr18
19  chr19
2   chr2
20  chr20
3   chr3
4   chr4
5   chr5
6   chr6
7   chr7
8   chr8
9   chr9
MT  chrM
X   chrX
Y   chrY