biology/vcf-split - The NetBSD Packages Collection

Split a multi-sample VCF into single-sample VCFs

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.

Build dependencies


Runtime dependencies

devel/libxtend biology/biolibc

Binary packages

NetBSD 8.0earmv7hfvcf-split-0.1.1.tgz
NetBSD 8.0i386vcf-split-0.1.1.tgz
NetBSD 8.0powerpcvcf-split-0.1.1.tgz
NetBSD 8.0powerpcvcf-split-0.1.1.tgz
NetBSD 8.0x86_64vcf-split-0.1.1.tgz
NetBSD 9.0aarch64vcf-split-0.1.1.tgz
NetBSD 9.0alphavcf-split-0.1.1.tgz
NetBSD 9.0earmv7hfvcf-split-0.1.1.tgz
NetBSD 9.0earmv7hfvcf-split-0.1.1.tgz
NetBSD 9.0i386vcf-split-0.1.1.tgz
NetBSD 9.0mips64ebvcf-split-0.1.1.tgz
NetBSD 9.0powerpcvcf-split-0.1.1.tgz
NetBSD 9.0powerpcvcf-split-0.1.1.tgz
NetBSD 9.0sparc64vcf-split-0.1.1.tgz
NetBSD 9.0sparcvcf-split-0.1.1.tgz
NetBSD 9.0x86_64vcf-split-0.1.1.tgz
NetBSD 9.0x86_64vcf-split-0.1.1.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


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.