Setup a configuration file

If you are planning to use gwas-norm or hpc-gwas-norm, then you will need to setup up a configuration file that can be located by gwas-norm and details where liftover chain files, the mapping files and an optional reference genome file are located. If you are using variant-mapper then you do not need a configuration file.

The configuration file is a simple .ini format.

# Convert to the same nomenclature
[assembly.synonyms]
grch38 = b38
b38 =    b38
hg38 =   b38
grch37 = b37
b37 =    b37
hg19 =   b37
hg37 =   b37
b36 =    b36
hg18 =   b36
hg36 =   b36
b35 =    b35
hg17 =   b35
hg35 =   b35
b34 =    b34
hg16 =   b34
hg34 =   b34

# Reference genome assemblies
[assembly.homo_sapiens]
assembly = b38
/lustre/projects/DTAdb/resources/human_genome/b38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

[assembly.homo_sapiens.b37]
assembly = b37
/lustre/projects/DTAdb/resources/human_genome/b37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz

[assembly.homo_sapiens.b36]
/lustre/projects/DTAdb/resources/human_genome/b36/Homo_sapiens.NCBI36.54.dna.toplevel.fa.gz

# Build/chain file mappings
[chain_files.b38]
b37 = /lustre/projects/DTAdb/resources/chain_files/GRCh38_to_GRCh37.chain.gz
b36 = /lustre/projects/DTAdb/resources/chain_files/GRCh38_to_NCBI36.chain.gz
b35 = /lustre/projects/DTAdb/resources/chain_files/GRCh38_to_NCBI35.chain.gz
b34 = /lustre/projects/DTAdb/resources/chain_files/GRCh38_to_NCBI34.chain.gz

[chain_files.b37]
b38 = /lustre/projects/DTAdb/resources/chain_files/GRCh37_to_GRCh38.chain.gz
b36 = /lustre/projects/DTAdb/resources/chain_files/GRCh37_to_NCBI36.chain.gz
b35 = /lustre/projects/DTAdb/resources/chain_files/GRCh37_to_NCBI35.chain.gz
b34 = /lustre/projects/DTAdb/resources/chain_files/GRCh37_to_NCBI34.chain.gz

[chain_files.b36]
b38 = /lustre/projects/DTAdb/resources/chain_files/NCBI36_to_GRCh38.chain.gz
b37 = /lustre/projects/DTAdb/resources/chain_files/NCBI36_to_GRCh37.chain.gz

[chain_files.b35]
b38 = /lustre/projects/DTAdb/resources/chain_files/NCBI35_to_GRCh38.chain.gz
b37 = /lustre/projects/DTAdb/resources/chain_files/NCBI35_to_GRCh37.chain.gz

[chain_files.b34]
b38 = /lustre/projects/DTAdb/resources/chain_files/NCBI34_to_GRCh38.chain.gz
b37 = /lustre/projects/DTAdb/resources/chain_files/NCBI34_to_GRCh37.chain.gz

# Mapping files
[mapping_files]
b38 = /lustre/projects/DTAdb/resources/mapping_files/b38/gwas_norm.common.biallelic.vep.b38.vcf.gz
b37 = /lustre/projects/DTAdb/resources/mapping_files/b37/gwas_norm.common.biallelic.vep.b37.vcf.gz