config4Small.tsv

JOBNAME	SomaticVariant
OUTDIR	/rdcw/fs1/dinglab/Active/Projects/yuweiz/projects/longreads_sv/test_out/test2/04_deepvariant/
SAMPLE	/rdcw/fs1/dinglab/Active/Projects/yuweiz/projects/longreads_sv/sample4SomaticVar.lst

#sample file should be in the below format:
#run_id	tumor_path	normal_path(if applicable).     #tab separated
#Carefully check your sample list, which determines the running mode (T-N matched or tumor only)

################# Clair3 ###################

PYTHON	/rdcw/fs1/dinglab/Active/Projects/yuweiz/anaconda3/envs/clair3/bin/python
PYPY	/rdcw/fs1/dinglab/Active/Projects/yuweiz/anaconda3/envs/clair3/bin/pypy3.6
SAMTOOLS	/rdcw/fs1/dinglab/Active/Projects/yuweiz/anaconda3/envs/py39/bin/samtools
PLATFORM	hifi_revio
#Select the sequencing platform of the input. Possible options {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, hifi_revio}.
THREAD	10
REF	/rdcw/fs1/dinglab/Active/Projects/yuweiz/data/human/hg38/GRCh38.p13.genome.fa







################### bsub ###################
GROUP	/yuweiz/default
QUEUE	general
#APP	docker(scao/dailybox)

#bsub -g /yuweiz/default -q general -n 1 -R "select[mem>30000] rusage[mem=30000]" -M 30000000 -a 'docker(scao/dailybox)' -o /rdcw/fs1/dinglab/Active/Projects/yuweiz/projects/longreads_sv/test_out/test2/gatk.log  -e /rdcw/fs1/dinglab/Active/Projects/yuweiz/projects/longreads_sv/test_out/test2/gatk.err bash /rdcw/fs1/dinglab/Active/Projects/yuweiz/projects/longreads_sv/test.cmd.sh
#samtools addreplacerg -r '@RG\tID:samplename\tSM:samplename' test2.minimap2.align.bam | samtools view -bS - >test.bam