snailqh/yono repository overview

sample=CHP000179
read1=CHP000179_primer_1.fq.gz
read2=CHP000179_primer_2.fq.gz
indir=CHP000179
outdir=out
capturekit=adultshealth-panel-Grch38.p12-6col.bed
thread=4
mymem=1

docker run  -v /testdata/CHP000179:/mnt/input -v /testdata/CHP000179:/mnt/output -v /testdata/database:/database $image /bin/bash /software/scripts/panel.sh

docker run  -it  -v $inputdir:/mnt/input -v $outputdir:/mnt/output -v $localref:/database -v $localannovar:/software/annovar/humandb/ $localdocker /bin/bash /software/scripts/wgs.sh $sample $read1 $read2 $thread $mem