hammerlab/concordance

Name: concordance

Owner: Hammer Lab

Description: Concordance between variant callers

Created: 2014-05-01 16:14:32.0

Updated: 2015-09-16 22:04:24.0

Pushed: 2014-11-27 03:26:14.0

Homepage: null

Size: 3442

Language: JavaScript

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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 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

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

Visualizing concordance across variant callers.

Visualizing scoring data across variant callers.