# 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.

Repository: https://github.com/broadinstitute/picard
Canonical: https://ross.abutalabs.com/products/broadinstitute-picard
Homepage: https://broadinstitute.github.io/picard/
Language: Java
License: MIT
License Family: permissive
Last push: 2026-07-31T19:58:00+00:00

## Health v2 (maintenance only)
Score: 85/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 95, release rhythm 63, longevity 100
- inputs: {"age_days": 4541, "days_push": 33, "days_rel": 33, "gap_med": 329.5, "n_releases_24m": 3}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1074, forks 383 (observed 2026-08-28T04:03:29.115633+00:00)

## What it is
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
- artifact type: cli-tool
- maturity: stable
- function: cli, developer-tools, data-science
- domain: bioinformatics, files
- platform: cli, jvm, cross-platform, windows
- tags: bioinformatics, sam-bam, cram, vcf, genomics, high-throughput-sequencing, htsjdk, java, command-line, linux, macos

## Member repositories
- broadinstitute/picard (main) score 85

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:03:29.115633+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T06:53:30.588523+00:00, confidence not recorded.
  - readme: https://github.com/broadinstitute/picard (fetched 2026-08-28T04:03:29.115633+00:00, sha 02c68cf782e8)
  - homepage: https://broadinstitute.github.io/picard/ (fetched 2026-08-29T12:55:06.723552+00:00, sha 20dd05b35453)
- Data as of 2026-08-30T08:39:29.467469+00:00.