Github.com/broadinstitute/switch-hitter/extract-eval-vcfs

Automatic Tools and Workflows
1

Switch Error Analysis Pipeline

Compare phasing accuracy between an evaluation callset and a truth callset, measuring switch error rates per sample per chromosome using WhatsHap.

Quick Start

1. Build Docker image

docker build -t switch-error-pipeline .

2. Run pilot test (single sample, chr20)

bash tests/test_pilot_samples.sh \
    --sample-id SAMPLE_ID \
    --truth-base gs://your-bucket/truth/ \
    --eval-base gs://your-bucket/eval/phased \
    --chrom 20
``
<hr>
<small>This is a companion discussion topic for the original entry at <a href='https://dockstore.org/workflows/github.com/broadinstitute/switch-hitter/extract-eval-vcfs'>github.com/broadinstitute/switch-hitter/extract-eval-vcfs</a></small>