global-config.txt

#This file ignores blank and commented ('#') lines.
#Values are noted as "<KEY>	<VALUE>"

#Path to snpEff installation
SNPEFF	/n/data1/hms/dbmi/park/cbohrson/installed/local/bin/snpEff

#Path to hg19 DBSNP database (necessary for shapeit only)
DBSNP_HG19	/n/data1/hms/dbmi/park/cbohrson/common_all_20160601.vcf.gz

#Path to downloaded 1000 genomes haplotype reference panel (necessary for shapeit only)
KGEN	/n/data1/hms/dbmi/park/cbohrson/1000GP

#Path to downloaded eagle directory (necessary for eagle only)
EAGLE	/n/data1/hms/dbmi/park/cbohrson/Eagle_v2.4

#Path to eagle hg19 reference panel (necessary for eagle only)
EAGLE_HG19_REF	/n/data1/hms/dbmi/park/cbohrson/EAGLE_HG19

#Path to eagle hg38 reference panel (necessary for eagle only)
EAGLE_HG38_REF	/n/data1/hms/dbmi/park/cbohrson/EAGLE_HG38

#Path to picard JAR file
PICARD	/n/data1/hms/dbmi/park/cbohrson/installed/local/bin/picard.jar

#Gap between SNPs required for regions to be chunked separately
GAP_REQUIREMENT	2000

#Target number of reads per LiRA job
READS_TARGET	10000

#Partition to submit to for parallelization
PARTITION	short

#Batch size for parallelization (number of scripts per job)
BATCH_SIZE	10

#Method to use for creating sSNV control curve of composite coverage vs. genome-wide sSNV rate.  Options are 'germline' (use germline sSNVs), 'general' (use all powered sites), or 'constant' (approximate true sSNV vs. composite-coverage relationship as constant). 'general' requires a genome file in the same directory as the reference.
CONTROL_METHOD	constant

#Script in $LIRA_DIR/scripts to use for parallelization
PARALLEL_SCRIPT	slurm.R

#Memory per slurm job in GB
MEMORY	2

#Wall time per slurm job in minutes
WALL_TIME	10

#Number of sampling replicates to use for CONTROL_METHOD
BOOTSTRAP_REPLICATES	100