recipe bcftools

BCFtools is a set of utilities that manipulate variant calls 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. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

Homepage

https://github.com/samtools/bcftools

License

GPL

Recipe

/bcftools/meta.yaml

Links

biotools: bcftools, usegalaxy-eu: bcftools_merge, doi: 10.1093/bioinformatics/btp352

package bcftools

Versions

1.11-0,  1.10.2-3,  1.10.2-2,  1.10.2-1,  1.10.2-0,  1.10.1-0,  1.10-0,  1.9-9,  1.9-8, 

1.11-0,  1.10.2-3,  1.10.2-2,  1.10.2-1,  1.10.2-0,  1.10.1-0,  1.10-0,  1.9-9,  1.9-8,  1.9-7,  1.9-6,  1.9-5,  1.9-4,  1.9-3,  1.9-2,  1.9-1,  1.8-3,  1.8-2,  1.8-1,  1.8-0,  1.7-0,  1.6-1,  1.6-0,  1.5-3,  1.5-2,  1.5-1,  1.5-0,  1.4.1-0,  1.4-0,  1.3.1-6,  1.3.1-5,  1.3.1-4,  1.3.1-3,  1.3.1-2,  1.3.1-1,  1.3.1-0,  1.3-5,  1.3-4,  1.3-3,  1.3-2,  1.3-1,  1.3-0,  1.2-4,  1.2-3,  1.2-2,  1.2-1,  1.2-0

Depends

• gsl >=2.6,<2.7.0a0

• htslib >=1.11,<1.12.0a0

• libgcc-ng >=7.5.0

• perl

• zlib >=1.2.11,<1.3.0a0

Required By

• lorikeet-genome

• metapop

• artic

• tb-profiler

• pathogen-profiler

• smoove

• chorus2

• ctat-mutations

• shigatyper

• phenix

• tetyper

• crispritz

• surpyvor

• uvp

• ariba

• connor

• phyluce

• drop

• trnanalysis

• riboseed

• chisel

• medaka

• snippy

• clair

• spliceai-wrapper

• vcfkit

• genotyphi

• ectyper

• bioconvert

• hap.py

• mutmap

• bcftools-gtc2vcf-plugin

• qtlseq

• sequana

• clsify

• gembs

• bcftools-snvphyl-plugin

• scalpel

• pbhoover

• pomoxis

• clever-toolkit

• cnv_facets

• phame

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bcftools

and update with:

conda update bcftools

or use the docker container:

docker pull quay.io/biocontainers/bcftools:<tag>

(see bcftools/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

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