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
Aug 24, 2024 6:50pm 0 VERSION_BUMP ad4c23c1
Feb 23, 2023 1:40am 0 VERSION_BUMP 3c47cb58
Feb 23, 2023 1:40am 0 VERSION_BUMP 8edbb7cd
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