wwliao / cnvnator

CNVnator Docker Image

CNVnator Docker Image

Run CNVnator on local machine

1. Pull CNVnator docker image

   docker pull wwliao/cnvnator
   

2. Extracting read mapping from BAM/SAM files

   docker run -v /path/to/workplace:/data wwliao/cnvnator -unique -root out.root -tree input.bam
   

3. Generating a histogram

   docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -his 500 -d /path/to/chrom/seqs
   

4. Calculating statistics

   docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -stat 500
   

5. RD signal partitioning

   docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -partition 500
   

6. CNV calling

   docker run -v /path/to/workplace:/data wwliao/cnvnator -root out.root -call 500 > out.call.txt
   

Run CNVnator on LSF cluster

1. 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
   

2. 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
   

3. 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
   

4. 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
   

5. 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