BSD Ports

biology/vcf-split 0.1.5.19 NetBSD

Split a multi-sample VCF into single-sample VCFs

System
NetBSD
Repository
pkgsrc
Maintainer
[email protected]
License
2-clause-bsd
Categories
biology
Package size
10.7 KiB, 24.2 KiB installed

Description

Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF with bcftools takes two days, so extracting the 137,977 samples one at a time or using thousands of parallel readers of the same file is impractical. Vcf-split solves this by generating thousands of single-sample outputs during a single sweep through the multi-sample input.

In the other systems

SystemPortVersion
NetBSDbiology/vcf-split0.1.5.19
FreeBSDbiology/vcf-split0.1.5.10_1
DragonFlybiology/vcf-split0.1.5.10_1
HardenedBSDbiology/vcf-split0.1.5.10_1
GhostBSDbiology/vcf-split0.1.5.10_1

Install

Binary package:

pkgin install vcf-split

From pkgsrc:

cd /usr/pkgsrc/biology/vcf-split && make install clean

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

RepositoryVersion
NetBSD 10.1 x86_640.1.5.19
NetBSD 10.1 aarch640.1.5.19
SmartOS / illumos x86_640.1.5.19
macOS 15 arm640.1.5.19

Dependencies

Run dependencies 1

No port depends on this one.