Picard Toolkit

Default Boolean Operator: Terms in a search string will be connected by the AND operator, EXAMPLE: searching genomic melanoma will produce the same results as genomic AND melanoma .
AND, OR, NOT: Combine terms in a search with the boolean operators AND (to add specificity), OR (to broaden), or NOT (to eliminate a term). Operators must be capitalized (all other search terms are not case-sensitive).
Wild Card: Add wild card symbols * (open-ended) and ? (single character) to truncate terms. EXAMPLE: searching gen* shows results for 'gene', 'genetic', 'genomic, etc. Searching gene? returns results for 'gene' or 'genes' but not for 'genome'.
Phrase Searching: Enclose search in quotation marks "keyword or search term" to search for an exact phrase. EXAMPLE: "transcription factors" returns results for records where transcription is immediately followed by the word factors .
Diacritics: Words containing diacritics translate those characters to non-diacritic form. EXAMPLE: massague returns results for Massague&#769 .
Filter by: Located on the homepage (left panel), use filters to search for records or narrow the search. From search results page, filters can be removed by clicking on the term at the top of the page.

UID: 11428

Publisher(s): Broad Institute

Description: Description from GitHub:

"A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.

Picard is implemented using the HTSJDK Java library HTSJDK to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM and VCF.

As of version 3.0, Picard requires Java 1.17."

Subject(s)

Access via GitHub
developer repository

Access via Broad Institute
user documentation
Access Restrictions: Free to All
Access Instructions: Available for download via GitHub under an MIT License
Associated Publications: Maciejowski J, Chatzipli A, Dananberg A, Chu K, Toufektchan E, Klimczak L, Gordenin D, Campbell P, de Lange T. APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis. Nature Genetics. 2020; 52(9):884-890.
Software Used: Gradle
open source build system

HTSJDK
Java library to support file formats

R
a free software environment for statistical computing and graphics.
Dataset Format(s): PDF, XML, TXT, MD, CSS, SH, JAVA
Dataset Size: 78 MB

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