broadinstitute/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. observed · 2026-10-09
Health v2 · maintenance only
79/100
- Activity 87
- Release rhythm 56
- Longevity 100
How is this computed?
round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10) — computed 2026-10-21. Adoption (stars, forks) is never an input.
- gap_med: 474
- age_days: 4589
- days_rel: 81
- days_push: 81
- n_releases_24m: 2
Adoption not part of the score
1080 stars · 384 forks observed · 2026-10-09
What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded
Picard is a set of Java command line tools from the Broad Institute for manipulating high-throughput sequencing data in formats such as SAM/BAM/CRAM and VCF. It is built on the HTSJDK library and distributed as a single executable jar.
Use cases
- manipulate SAM/BAM/CRAM alignment files
- validate and clean up VCF variant files
- mark duplicate reads in BAM files
- convert between sequencing file formats
- collect metrics from sequencing data
- process high-throughput sequencing data in pipelines
When to choose
- you need reliable, widely-adopted tools for SAM/BAM/CRAM or VCF manipulation
- you are building genomics pipelines (e.g. with GATK or WDL workflows)
- you want a JVM-based alternative to samtools with rich metrics tools
When to avoid
- you need a lightweight C binary you can add directly to PATH
- your workflow is not Java/JVM-friendly
- you need interactive visualization of sequencing data rather than command-line manipulation
Facets
cli-tool · maturity stable
cli developer-tools data-science bioinformatics files cli jvm cross-platform windows bioinformatics sam-bam cram vcf genomics high-throughput-sequencing htsjdk java command-line linux macos
2 sources
- readme: https://github.com/broadinstitute/picard · fetched 2026-10-09 · 02c68cf782e8
- homepage: https://broadinstitute.github.io/picard/ · fetched 2026-08-29 · 20dd05b35453
Member repositories
| Repository | Role | Health v2 |
|---|---|---|
| broadinstitute/picard | main | 79 |
For agents
markdown · JSON · MCP: product_card(name="broadinstitute/picard")
Data as of 2026-10-19T08:05:51.212177+00:00 · Report a problem