https://github.com/hammerlab/concordance

Concordance between variant callers
https://github.com/hammerlab/concordance

Last synced: 4 months ago
JSON representation

Concordance between variant callers

• Host: GitHub
• URL: https://github.com/hammerlab/concordance
• Owner: hammerlab
• License: apache-2.0
• Created: 2014-05-01T16:14:32.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2014-11-27T03:26:14.000Z (over 11 years ago)
• Last Synced: 2025-04-26T07:35:27.091Z (about 1 year ago)
• Language: JavaScript
• Size: 3.28 MB
• Stars: 17
• Watchers: 8
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# Concordance

Visualize concordance and other quality metrics between variant callers.

Usage:

    concordance_counter.py [-h] [-o output] sample-name truth.vcf

                           vcfname=file.vcf [vcfname=file.vcf ...]

    open concordance.html

For example, to reproduce the sample data included in the repo, run:

    concordance_counter.py tumor.chr20 sampledata/trn.truth.chr20.vcf.gz \

      somatic-sniper=sampledata/trn.somaticsniper.20140508.chr20.derivedFA.vcf \

      mutect=sampledata/trn.mutect.20140505.chr20.vcf \

      strelka=sampledata/trn.strelka.20140508.chr.20.derivedFA.vcf \

      varscan=sampledata/trn.varscan.05142014.chr20.hc.derivedFA.vcf \

      > viewer/concordance-data.js

## Setting up

We use [virtualenv](https://pypi.python.org/pypi/virtualenv) for dependency management.

To get started, run:

    virtualenv env                   # make a new virtualenv named 'env'.

    source env/bin/activate          # activate the env (local pip, python).

    pip install -r requirements.txt  # install the requirements in the env.

## Examples

![](http://link.isaachodes.io/image/3v362B0g1t3B/Screen%20Shot%202014-05-22%20at%204.57.29%20PM.png)

Visualizing calls made against read depth and frequency of variant allele, for all callers.

![](http://link.isaachodes.io/image/003d052e053b/Screen%20Shot%202014-05-22%20at%204.58.00%20PM.png)

Visualizing concordance across variant callers.

![](http://link.isaachodes.io/image/383244063D1q/Screen%20Shot%202014-05-22%20at%204.59.16%20PM.png)

Visualizing scoring data across variant callers.