config.yaml

# Harmonisation configuration

# =======================
# Desired genome assembly *use value from table below*
# e.g. '38' if desired assembly is 'GRCh38'
#
# value | UCSC  | GRC
# ========================
# '28'  |'hg10' | 'NCBI28'
# '29'  |'hg11' | 'NCBI29'
# '30'  |'hg13' | 'NCBI30'
# '31'  |'hg14' | 'NCBI31'
# '33'  |'hg15' | 'NCBI33'
# '34'  |'hg16' | 'NCBI34'
# '35'  |'hg17' | 'NCBI35'
# '36'  |'hg18' | 'NCBI36'
# '37'  |'hg19' | 'GRCh37'
# '38'  |'hg38' | 'GRCh38'

desired_build: '38'

# ========================

chromosomes: ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y', 'MT']
remote_vcf_location: 'ftp://ftp.ensembl.org/pub/current_variation/vcf/homo_sapiens/'
# Change below for other releases of Ensembl
remote_ensembl_variation: 'ftp://ftp.ensembl.org/pub/current_mysql/homo_sapiens_variation_100_38/'
# Make sure you have a trailing slash ('/') on the path below
local_resources: resources/

repo_path: ./

# ========================
# Percentage of variants that need to conform to 
# a particular direction, in order to have strand
# consensus. 

threshold: 0.99

# =======================
# Set local_synonyms: True if you want to build a
# local table of rsID synonyms to use for the qc.
# If you set local_synonyms: False synonyms will be
# checked against the Ensembl REST API, which is
# rate limited adn far slower. The local table 
# requires 52GB storage (Ensembl 100) but expect 
# it to require more space.

local_synonyms: True