input=/small20.vcf.gz
fileId=5
aggregated=NONE
studyType=COLLECTION
studyName=studyName
studyId=7
outputDir=/tmp
pedigree=
dbCollectionVariantsName=variants
dbCollectionFilesName=files
dbName=variantJob
storageEngine=mongodb
compressGenotypes=true
compressExtension=.gz
includeSrc=FIRST_8_COLUMNS

opencga.app.home=

skipLoad=false

#VEP
vepInput=/tmp/preannot_TEST.tsv
vepOutput=/tmp/variants.annot.tsv.gz
vepPath=
vepCacheDirectory=/path/to/cache
vepCacheVersion=79
vepSpecies=homo_sapiens
vepFasta=/path/to/file.fa
vepNumForks=4


# Repeat steps
# true: The already COMPLETEd steps will be rerun. This is restarting the job from the beginning
# false(default): if the job was aborted and is relaunched, COMPLETEd steps will NOT be done again
allowStartIfComplete=false

readPreference=primary
input=/small20.vcf.gz
fileId=5
aggregated=NONE
studyType=COLLECTION
studyName=studyName
studyId=7
outputDir=/tmp
pedigree=
dbCollectionVariantsName=variants
dbCollectionFilesName=files
dbName=variantJob
storageEngine=mongodb
compressGenotypes=true
compressExtension=.gz
includeSrc=FIRST_8_COLUMNS

opencga.app.home=/opt/opencga

skipLoad=false

#VEP
vepInput=/tmp/preannot_TEST.tsv
vepOutput=/tmp/variants.annot.tsv.gz
vepPath=
vepCacheDirectory=/path/to/cache
vepCacheVersion=79
vepSpecies=homo_sapiens
vepFasta=/path/to/file.fa
vepNumForks=4


# Repeat steps
# true: The already COMPLETEd steps will be rerun. This is restarting the job from the beginning
# false(default): if the job was aborted and is relaunched, COMPLETEd steps will NOT be done again
allowStartIfComplete=false

readPreference=primary
Set opencga value to /opt/opencga
Set opencga value to /opt/opencga
