biology/beagle - The NetBSD Packages Collection

Phasing genotypes and imputing ungenotyped markers 

Beagle is a software package for phasing genotypes and for imputing
ungenotyped markers.

The Beagle 5.2 genotype imputation method is described in:

B L Browning, Y Zhou, and S R Browning (2018). A one-penny imputed
genome from next generation reference panels. Am J Hum Genet
103(3):338-348. doi:10.1016/j.ajhg.2018.07.015

The most recent reference for Beagle's phasing method is:

S R Browning and B L Browning (2007) Rapid and accurate haplotype
phasing and missing data inference for whole genome association
studies by use of localized haplotype clustering. Am J Hum Genet
81:1084-1097. doi:10.1086/521987

Build dependencies

pkgtools/mktools pkgtools/cwrappers

Runtime dependencies

lang/openjdk17 lang/openjdk17

Binary packages

OSArchitectureVersion
NetBSD 10.0aarch64beagle-5.2.tgz
NetBSD 10.0aarch64beagle-5.2.tgz
NetBSD 10.0earmv6hfbeagle-5.2.tgz
NetBSD 10.0earmv6hfbeagle-5.2.tgz
NetBSD 10.0earmv6hfbeagle-5.2.tgz
NetBSD 10.0earmv7hfbeagle-5.2.tgz
NetBSD 10.0earmv7hfbeagle-5.2.tgz
NetBSD 10.0earmv7hfbeagle-5.2.tgz
NetBSD 10.0i386beagle-5.2.tgz
NetBSD 10.0i386beagle-5.2.tgz
NetBSD 10.0powerpcbeagle-5.2.tgz
NetBSD 10.0powerpcbeagle-5.2.tgz
NetBSD 10.0powerpcbeagle-5.2.tgz
NetBSD 10.0sparc64beagle-5.2.tgz
NetBSD 10.0sparc64beagle-5.2.tgz
NetBSD 10.0x86_64beagle-5.2.tgz
NetBSD 10.0x86_64beagle-5.2.tgz
NetBSD 9.0aarch64beagle-5.2.tgz
NetBSD 9.0aarch64beagle-5.2.tgz
NetBSD 9.0alphabeagle-5.2.tgz
NetBSD 9.0alphabeagle-5.2.tgz
NetBSD 9.0earmv6hfbeagle-5.2.tgz
NetBSD 9.0earmv6hfbeagle-5.2.tgz
NetBSD 9.0earmv6hfbeagle-5.2.tgz
NetBSD 9.0earmv7hfbeagle-5.2.tgz
NetBSD 9.0earmv7hfbeagle-5.2.tgz
NetBSD 9.0earmv7hfbeagle-5.2.tgz
NetBSD 9.0i386beagle-5.2.tgz
NetBSD 9.0i386beagle-5.2.tgz
NetBSD 9.0powerpcbeagle-5.2.tgz
NetBSD 9.0powerpcbeagle-5.2.tgz
NetBSD 9.0powerpcbeagle-5.2.tgz
NetBSD 9.0x86_64beagle-5.2.tgz
NetBSD 9.0x86_64beagle-5.2.tgz
NetBSD 9.3x86_64beagle-5.2.tgz

Binary packages can be installed with the high-level tool pkgin (which can be installed with pkg_add) or pkg_add(1) (installed by default). The NetBSD packages collection is also designed to permit easy installation from source.

Available build options

(none)

Known vulnerabilities

The pkg_admin audit command locates any installed package which has been mentioned in security advisories as having vulnerabilities.

Please note the vulnerabilities database might not be fully accurate, and not every bug is exploitable with every configuration.

Problem reports, updates or suggestions for this package should be reported with send-pr.