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Pull CNVnator docker image
docker pull wwliao/cnvnator -
Extracting read mapping from BAM/SAM files
docker run -v /path/to/workplace:/data wwliao/cnvnator -unique -root out.root -tree input.bam -
Generating a histogram
docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -his 500 -d /path/to/chrom/seqs -
Calculating statistics
docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -stat 500 -
RD signal partitioning
docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -partition 500 -
CNV calling
docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -call 500 > out.call.txt
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Extracting read mapping from BAM/SAM files
LSF_DOCKER_PRESERVE_ENVIRONMENT=false LSF_DOCKER_VOLUMES="/path/to/workplace:/data" bsub -q research-hpc -a "docker(wwliao/cnvnator)" cnvnator -unique -root out.root -tree input.bam -
Generating a histogram
LSF_DOCKER_PRESERVE_ENVIRONMENT=false LSF_DOCKER_VOLUMES="/path/to/workplace:/data" bsub -q research-hpc -a "docker(wwliao/cnvnator)" cnvnator -root out.root -his 500 -d /path/to/chrom/seqs -
Calculating statistics
LSF_DOCKER_PRESERVE_ENVIRONMENT=false LSF_DOCKER_VOLUMES="/path/to/workplace:/data" bsub -q research-hpc -a "docker(wwliao/cnvnator)" cnvnator -root out.root -stat 500 -
RD signal partitioning
LSF_DOCKER_PRESERVE_ENVIRONMENT=false LSF_DOCKER_VOLUMES="/path/to/workplace:/data" bsub -q research-hpc -a "docker(wwliao/cnvnator)" cnvnator -root out.root -partition 500 -
CNV calling
LSF_DOCKER_PRESERVE_ENVIRONMENT=false LSF_DOCKER_VOLUMES="/path/to/workplace:/data" bsub -q research-hpc -oo out.call.txt -a "docker(wwliao/cnvnator)" cnvnator -root out.root -call 500