config4StrucVar.tsv

JOBNAME	SVcall
OUTDIR	/rdcw/fs1/dinglab/Active/Projects/yuweiz/projects/longreads_sv/test_out
SAMPLE	/rdcw/fs1/dinglab/Active/Projects/yuweiz/projects/longreads_sv/sample4StrucVar.lst

	#sample file should be in the below format:
	#id sequencing_platform input_path

################## parameter ##################
MINIMAP2	/rdcw/fs2/home1/Active/home/yuweiz/anaconda3/envs/longread_sv/bin/minimap2
#minimap2 = 2.19
SNIFFLES	/rdcw/fs2/home1/Active/home/yuweiz/anaconda3/envs/longread_sv/bin/sniffles
#SNIFFLES = 2.0.7
GATK	gatk
	#/rdcw/fs1/dinglab/Active/Projects/yuweiz/anaconda3/bin/gatk

SAMTOOLS	samtools
THREAD	12
SNIFFLES_MODE	Both
	#Sniffles can predict SVs in two modes, basic and mosaic. Options: Both/Basic/Mosaic

################## index ##################
INDEX	/rdcw/fs1/dinglab/Active/Projects/yuweiz/data/human/hg38/minimap2/hg38.mmi
REF	/rdcw/fs1/dinglab/Active/Projects/yuweiz/data/human/hg38/GRCh38.p13.genome.fa


################## GATK germline mutation ###################
PLOIDY	1
MIN_MAP_Q	30
MIN_BASE_Q	20


################### bsub ###################
GROUP	/yuweiz/default
QUEUE	general