picard-tools ☆

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Description:
Tools for manipulating HTS data and formats

Type: Formula | Tracked Since: Dec 28, 2025

Links: Homepage | formulae.brew.sh

Category: Other

Tags: bioinformatics hts genomics bam samtools

Install: brew install picard-tools

About:
Picard Tools is a command-line Java-based toolkit for manipulating high-throughput sequencing (HTS) data and formats. It provides a comprehensive suite of utilities to process SAM/BAM/CRAM files, including sorting, marking duplicates, and generating metrics. Its main value is ensuring data quality and preparing datasets for downstream analysis in bioinformatics pipelines.

Key Features:

SAM/BAM/CRAM file manipulation and conversion
Duplicate marking and quality control metrics
Sequence data filtering and interval processing
Library-level utilities for genomic data handling

Use Cases:

Preparing aligned sequencing data for variant calling
Quality control and duplicate removal in NGS pipelines
Converting between HTS file formats

Alternatives:

SAMtools – SAMtools is a C-based toolkit focused on indexing and variant calling, while Picard complements it with advanced data manipulation and metrics generation.
GATK – GATK includes many Picard functions natively, but the standalone Picard tool is often used for preprocessing steps outside the GATK framework.

Version History

Detected	Version	Rev	Change	Commit
Oct 9, 2024 10:36pm		0	VERSION_BUMP	d4b3b2be
Oct 9, 2024 9:45pm		0	VERSION_BUMP	94cea61e