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:

1.15.1-0,  1.15-2,  1.15-1,  1.15-0,  1.14-1,  1.14-0,  1.13-0,  1.12-1,  1.12-0, 

1.15.1-0,  1.15-2,  1.15-1,  1.15-0,  1.14-1,  1.14-0,  1.13-0,  1.12-1,  1.12-0,  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,  1.5-4,  1.5-3,  1.5-2,  1.5-1,  1.5-0,  1.4.1-0,  1.4-0,  1.3.1-7,  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,  1.3-7,  1.3-6,  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 >=2.7,<2.8.0a0

• htslib >=1.15,<1.16.0a0

• libgcc-ng >=10.3.0

• libzlib >=1.2.11,<1.3.0a0

• perl

• zlib >=1.2.11,<1.3.0a0

Required By:

• pggb

• smoove

• genotyphi

• trnanalysis

• vcfkit

• cnv_facets

• contatester

• vsnp3

• bcftools-snvphyl-plugin

• riboseed

• svdss

• clever-toolkit

• consplice

• hap.py

• nanocaller

• uvp

• spliceai-wrapper

• annotwg

• chorus2

• hatchet

• gridss

• shigatyper

• medaka

• phyluce

• connor

• harvest-variants

• pomoxis

• ariba

• jbrowse2

• surpyvor

• ngs_te_mapper2

• bcftools-gtc2vcf-plugin

• ctat-mutations

• phenix

• qtlseq

• drop

• ectyper

• mutmap

• pathogen-profiler

• ngscheckmate

• snippy

• bioconvert

• bacgwasim

• tbpore

• snakesv

• telr

• tetyper

• duet

• chisel

• crispritz

• isafe

• phame

• seroba

• scalpel

• metapop

• artic

• lorikeet-genome

• pbhoover

• clsify

• gembs

• clair

Installation

With an activated Bioconda channel (see 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>)

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