################################################################################
##
## Copyright (c) 2007-2011 Illumina, Inc.
##
## This software is covered by the "Illumina Genome Analyzer Software 
## License Agreement" and the "Illumina Source Code License Agreement", 
## and certain third party copyright/licenses, and any user of this 
## source file is bound by the terms therein (see accompanying files
## Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
## Illumina_Source_Code_License_Agreement.pdf and third party 
## copyright/license notices).
##
## This file is part of the Consensus Assessment of Sequence And VAriation
## (CASAVA) software package.
##
## file ValidationConfig.mk
##
## brief Example validation dataset configuration 
##
## author Roman Petrovski
##
################################################################################

BUILD_PARAMS:= \
--samtoolsRefFile /home/psgendb/local/pkg/CASAVA_v1.8.2-build/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/chr22.fa \
--refFlatFile /home/psgendb/local/pkg/CASAVA_v1.8.2-build/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Annotation/Genes/refFlat.txt.gz \
--applicationType RNA \
--variantsNoCovCutoff \
--indelsSaveTempFiles \
--inSampleDir $(ALIGNED_ROOT)/Project_Demo/Sample_AR008