https://github.com/poisonalien/varscan_accessories

accessory scripts for processing varscan somatic/copynumber outputs.
https://github.com/poisonalien/varscan_accessories

converts-varscan-somatic copynumber segmentation somatic-variants varscan vcf

Last synced: 8 days ago
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accessory scripts for processing varscan somatic/copynumber outputs.

• Host: GitHub
• URL: https://github.com/poisonalien/varscan_accessories
• Owner: PoisonAlien
• License: mit
• Created: 2016-01-11T08:35:18.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2017-12-08T06:07:40.000Z (over 7 years ago)
• Last Synced: 2025-04-20T13:37:17.565Z (about 1 month ago)
• Topics: converts-varscan-somatic, copynumber, segmentation, somatic-variants, varscan, vcf
• Language: Python
• Homepage:
• Size: 9.77 KB
• Stars: 9
• Watchers: 2
• Forks: 10
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
#### Command line accessory scripts for processing varscan somatic/copynumber outputs.

`vs_format_converter.py` converts varscan somatic output from vcf to snp and vice-versa 

`vs_indel_to_annovar.py` converts varscan somatic indels to annovar input. 

`dnaCopyScan.R` Takes output from varscan copynumber command (.copynumber) and performs CBS segmentation.