PARAMETERS

source CORES

# GENERAL OPTIONS
THREADS=30
JOBBINS=5 
DATASOURCE=Data
REFERENCEFILE=/home/ozank/Analysis/NGS-Pipeline/Dmel_mtDNA_ref_v6.fasta
READ1EXTENSION="_R1.fastq.gz"
READ2EXTENSION="_R2.fastq.gz"

# JAVA OPTIONS
# Heap size should be set to a value below (AVAILBLE_RAM/THREADS)
HEAPSIZE="-Xmx2g"
# Garbage collector should be set according to: https://www.oracle.com/webfolder/technetwork/tutorials/obe/java/gc01/index.html
GARBAGECOLLECTOR="-XX:ParallelGCThreads=$JAVAGCCORES"
JAVAOPTIONS="$HEAPSIZE $GARBAGECOLLECTOR"

# TEMPFILES takes the following options: 
# "K" for Keep
# "A" for Archive 
# "D" for Deletion 
ARCHIVEFILES="A"
ARCHIVEDIR=/home/Ext3-8TB/ozank/Migration2018/Final

# TRIMMING OPTIONS
TRIMQUALITY=25
ADAPTER1="AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"
ADAPTER2="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
CLIP5_R1=10
CLIP5_R2=10
CLIP3_R1=12
CLIP3_R2=12
TRIMGALOREOPTIONS="--fastqc --cores $TRIMCORES -a $ADAPTER1 -a2 $ADAPTER2 --paired -q $TRIMQUALITY --retain_unpaired --clip_R1 $CLIP5_R1 --clip_R2 $CLIP5_R2 --three_prime_clip_R1 $CLIP3_R1 --three_prime_clip_R2 $CLIP3_R2 "


# ALIGNING OPTIONS
BWAMINSCOREOUTPUT=30
BWABATCHSIZE=10000000
BWAOPTIONS="-t $BWACORES -K $BWABATCHSIZE  -T $BWAMINSCOREOUTPUT "


# RGTAGS
RGTAGFILE=RGTAGS
ADDGROUPOPTIONS="VALIDATION_STRINGENCY=STRICT CREATE_INDEX=false" 

# VARIANT CALLING OPTIONS
SCALEMAPQ=50
BASEQUALMIN=20
VARQUALMIN=20
MAXDEPTH=2000

BCFMPILEUPOPTIONS="-B -C$SCALEMAPQ -q$BASEQUALMIN -Q$VARQUALMIN -d$MAXDEPTH -a AD,DP,SP,INFO/AD -Ou"
BCFCALLOPTIONS="-m -A -v -Ov"

VCFOUTPUTFILENAME="Migration2018-dmel-pool-Final"