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config.yaml
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---
# Reference assemblies (genomes)
hs37fasta: /media/mrueda/8TB/Databases/genomes/hs37d5.fa.gz
hg19fasta: /media/mrueda/8TB/Databases/genomes/ucsc.hg19.fasta.gz
hg38fasta: /media/mrueda/8TB/Databases/genomes/hg38.fa.gz
# ClinVar
hg19clinvar: /media/mrueda/8TB/Databases/snpeff/v5.0/hg19/clinvar_20211218.vcf.gz
hg38clinvar: /media/mrueda/8TB/Databases/snpeff/v5.0/hg38/clinvar_20211218.vcf.gz
# Cosmic
hg19cosmic: /media/mrueda/8TB/Databases/snpeff/v5.0/hg19/CosmicCodingMuts.normal.hg19.vcf.gz
hg38cosmic: /media/mrueda/8TB/Databases/snpeff/v5.0/hg38/CosmicCodingMuts.normal.hg38.vcf.gz
# dbSNSFP Academic
hg19dbnsfp: /media/mrueda/8TB/Databases/snpeff/v5.0/hg19/dbNSFP4.1a_hg19.txt.gz
hg38dbnsfp: /media/mrueda/8TB/Databases/snpeff/v5.0/hg38/dbNSFP4.1a_hg38.txt.gz
# Miscellanea software
snpeff: /pro/NGSutils/snpEff/snpEff.jar
snpsift: /pro/NGSutils/snpEff/SnpSift.jar
bcftools: /pro/NGSutils/bcftools-1.15.1/bcftools
# Max RAM memory for snpeff (optional)
mem: 8G
# Temporary directory (optional)
tmpdir: /media/mrueda/8TB/tmp
# MongoDB
mongoimport: /home/mrueda/Soft/mongodb-database-tools-ubuntu2004-x86_64-100.5.1/bin/mongoimport
mongostat: /home/mrueda/Soft/mongodb-database-tools-ubuntu2004-x86_64-100.5.1/bin/mongostat
mongodburi: mongodb://root:[email protected]:27017/beacon?authSource=admin
mongosh: /usr/bin/mongosh
# Set of fields from dbSNSFP (optional)
dbnsfpset: all