openeuler/survivor repository overview

⁠Quick reference

• The official SURVIVOR docker image.

• Maintained by: openEuler CloudNative SIG⁠.

• Where to get help: openEuler CloudNative SIG⁠, openEuler⁠.

⁠survivor | openEuler

SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

Learn more on SURVIVOR⁠.

⁠Supported tags and respective Dockerfile links

The tag of each survivor docker image is consist of the version of survivor and the version of basic image. The details are as follows

⁠Usage

Here, users can select the corresponding {Tag} by requirements.

• Pull the openeuler/survivor image from docker

  docker pull openeuler/survivor:{Tag}
  

  Copy

• Start an interactive survivor instance

  docker run -it --name my-survivor openeuler/survivor:{Tag}
  

  Copy

• Merge and compare SVs across VCF files. First collect all VCF files to merge in a file, then use SURVIVOR merge with a maximum allowed distance of 1kb and a minimum support of 2 callers that must agree on the type and strand of the SV

  ls *.vcf > /data/vcf_files.txt
  docker run --rm -v /path/to/data:/data openeuler/survivor:{Tag} SURVIVOR merge /data/vcf_files.txt 1000 2 1 1 0 30 /data/merged.vcf
  

  Copy

• Check the logs of the running container

  docker logs -f my-survivor
  

  Copy

• Execute a SURVIVOR command in the running container

  docker exec -it my-survivor SURVIVOR
  

  Copy

⁠Question and answering

If you have any questions or want to use some special features, please submit an issue or a pull request on openeuler-docker-images⁠.