parameters_template.txt

; NAME OF FILE CONTAINING LOGS
LOGFILE=<PREFIX>_logfile_fastgbs.log

; FLOWCELL INFORMATION
FLOWCELL=<FLOWCEL>

; LANES INFORMATION
CD5NCANXX_LANES=<LANE>

; SEQUENCING TECHNOLOGY: ILLUMINA IONTORRENT
TECHNOLOGY=ILLUMINA

; SEQUENCE TYPE: SE (Single End) or PE (Paired Ends)
SEQTYPE=SE

; NAME OF THE REFERENCE GENOME FILES --> PREFIX YOU CHOSE + .fa
REFGEN=<PREFIX>.fa

; SEQUENCE USED FOR ADAPTOR RECOGNITION (THE COMPLETE ADAPTOR SEQUENCE IS
; AGATCGGAAGAGCGGG)
ADAPFOR=AGATCGGAAG

; IF PAIRED END READS, ADD ADAPTER SEQUENCE IN REVERSE SEQUENCE (R2)
ADAPREV=AGATCGGAAG

; MINIMUM READ LENGTH TO KEEP
READLEN=50

; NUMBER OF PARALLEL PROCESS FOR BWA
BWAPAR=4

; NUMBER OF THREAD FOR EACH BWA PROCESS
BWATHR=4

; MAXIMUM NUMBER OF CORES THAT COULD BE ALLOWED BY YOUR COMPUTER FOR THIS ANALYSIS
; SHOULD BE EQUAL TO: BWAPAR X BWATHR
NBCOR=16

; OPTION TO MOVE SAMPLES WITH LESS THAN 10% THE AVERAGE NUMBER OF SAMPLES IN THE POOL: YES or NO
MVSAMPLES=YES

; OPTION TO SAVE DISK SPACE; DELETE INTERMEDIARY FILES: NO or YES
DELFILES=YES
DELLIST=*.fq *.sam *.temp.bam *.unknown.barcodes

; NAME OF FILE CONTAINING LIST OF S1.BAM FILE FOR PLATYPUS ANALYSIS 
BAMLIST=List_bam

; VARIANT CALING FROM A DATABASE: None or vcf file
SOURCE=None

; FOR PLATYPUS: Minimum number of supporting reads required before a
; variant candidate will be considered (equivalent to minDP in vcftools)
MINREADS=2

; PLATYPUS LOGFILE
LOGPLAT=<PREFIX>_FastGBS_platypus_log.txt

;PROPORTION OF MISSING DATA (0 to 1 (no missing data)) AND MAF (minimum allele frequency, 0 to 1)
MAX-MISSING=0.2
MAF=0.01

; PLATYPUS OUTPUT VCF FILE
OUTPLAT=<PREFIX>_FastGBS_platypus