#This config file is a very complete one, going from pair-end FASTQ files to a cleaned VCF, and cleaning intermediate data
$order
1=fastqc
2=cutadapt
3=bwaAln
4=bwaSampe
5=picardToolsSortSam
6=samtoolsflagstat
7=samtoolsview
8=samToolsIndex
9=gatkRealignerTargetCreator
10=gatkIndelRealigner
11=picardToolsMarkDuplicates
1000=gatkHaplotypeCaller
1001=gatkVariantFiltration
1002=gatkSelectVariants
$cleaner
3
4
9
#PUT YOUR OWN SCHEDULER CONFIGURATION HERE
#Example for SGE
#$sge
#-q YOURQUEUE.q
#-b Y
$cutadapt
-O=10
-m=35
-q=20,20
--overlap=7
# Adaptator1 is removed in the forward (-b) and reverse (-B) reads (5' and 3' position)
-b ADAPTATOR1REVERSE -B ADAPTATOR1REVERSE
# Same traitement is done for the forward adaptator sequence
-b ADAPTATOR1FORWARD -B ADAPTATOR1FORWARD
$bwa aln
-n=5
$bwa sampe
-a 500
$picardToolsSortSam
SORT_ORDER=coordinate
VALIDATION_STRINGENCY=SILENT
CREATE_INDEX=TRUE
$samToolsView
-h
-b
-f=0x02
$gatkRealignerTargetCreator
-T=RealignerTargetCreator
$gatkIndelRealigner
-T=IndelRealigner
$picardToolsMarkDuplicates
VALIDATION_STRINGENCY=SILENT
CREATE_INDEX=TRUE
REMOVE_DUPLICATES=TRUE
$gatkHaplotypeCaller
-T=HaplotypeCaller
-rf BadCigar
$gatkVariantFiltration
-T=VariantFiltration
--filterName 'FILTER-DP' --filterExpression 'DP<10 || DP>600' --filterName 'LowQual' --filterExpression 'QUAL<30'
$gatkSelectVariants
-T=SelectVariants
-selectType=SNP