
## tools
PICARD=@PATH@/bin/picard/picard-tools-1.106
SAMTOOLS=@PATH@/bin/samtools/samtools-0.1.19
GATK=@PATH@/bin/gatk/GenomeAnalysisTK-1.6-9-g47df7bb
BCFTOOLS=@PATH@/bin/samtools/samtools-0.1.19/bcftools
TABIX=@PATH@/bin/tabix/tabix-0.2.6
ANNOVAR=</path/to/annovar>
ANNOVARDB=</path/to/annovardb>
SCRIPT_PATH=@PATH@/src


###execultables
JAVA=@JAVA@
PERL=@PERL@

### references
REF_GENOME=@PATH@/resources/allchr.hg19.fa
dbSNP_REF=@PATH@/resources/dbsnp.vcf.gz
REFSEQ_UNIPORT=@PATH@/resources/RefSeq_Uniprot_mapping_table.txt
HUMAN_DOMAIN_CORR=@PATH@/resources/Human_domain_coordinates.txt

### flags and paramters
REALIGNEMNT=YES
RECALIBRATION=YES
ALIGNER=TOPHAT:BWA
PROTEOMICS=YES
TEMPORARY_FILES_REMOVE=NO
CHR_INDEX=1:2:3:4:5:6:7:8:9:10:11:12:13:14:15:16:17:18:19:20:21:22:X:Y:M
JVM_MEM=-Xmx10g -Xms5g

### CUSTOMIZED PARAMTERS 
HIGH_ReadRankPosSum=8
LOW_ReadRankPosSum=-8  
MIN_ALT_READS=3
MIN_READ_DEPTH=3
R_CUTOFF=0.1
R_CUTOFF2=0.05
KEEP_ALL_SNV=T



