./biology/bcftools, Calling and manipulating files VCF and BCF formats

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Branch: CURRENT, Version: 1.9, Package name: bcftools-1.9, Maintainer: bacon

BCFtools is a program for variant calling and manipulating files in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
In order to avoid tedious repetion, throughout this document we will use "VCF"
and "BCF" interchangeably, unless specifically noted.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.


Required to run:
[lang/python27] [biology/htslib]

Required to build:
[pkgtools/cwrappers]

Master sites:

SHA1: 9b649c3f407528ee193210f68b8e21e8b0aebf31
RMD160: 59b9997aaa509ba84c41b7e78821f31eca8d90dc
Filesize: 3060.894 KB

Version history: (Expand)


CVS history: (Expand)


   2019-03-27 16:58:38 by Jason Bacon | Files touched by this commit (1)
Log message:
biology/bcftools: Add zlib dependency for Linux

Resolves build failures on CentOS
   2018-11-15 10:21:24 by Adam Ciarcinski | Files touched by this commit (4)
Log message:
bcftools: added version 1.9

BCFtools is a program for variant calling and manipulating files in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
In order to avoid tedious repetion, throughout this document we will use \ 
"VCF"
and "BCF" interchangeably, unless specifically noted.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.