Bcftools - Revision history

Rf at 17:31, 25 February 2017

2017-02-25T17:31:38Z

Rf at 17:06, 25 February 2017

2017-02-25T17:06:28Z

Rf at 16:55, 25 February 2017

2017-02-25T16:55:29Z

Rf: Created page with "= Introduction = This is a VCF manipulation suite from Heng Li, author of samtools. It is included in the samtools package, but is not a series of subcommands under samtools,..."

2017-02-25T16:27:10Z

Created page with "= Introduction = This is a VCF manipulation suite from Heng Li, author of samtools. It is included in the samtools package, but is not a series of subcommands under samtools,..."

New page

= Introduction =

This is a VCF manipulation suite from Heng Li, author of samtools. It is included in the samtools package, but is not a series of subcommands under samtools, rather it is an independent set of tools which are activated by its own subcommands unde the main command '''bcftools'''.

Note that it was only capable of a few subcommands before version 0.1.2 (i.e. versions 0.1.19 and before). However from 1.2 onwards it has many more new subcommands.

= Usage =

The '''bcftools filter''' capability is one of the new tools from bcftools v1.2

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	The '''bcftools filter''' capability is one of the new tools from bcftools v1.2		The '''bcftools filter''' capability is one of the new tools from bcftools v1.2
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		+	= Links =
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		+	* [https://samtools.github.io/bcftools/bcftools.html hompage with manual]

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	Note that it was only capable of a few subcommands before version 0.1.2 (i.e. versions 0.1.19 and before). However from 1.2 onwards it has many more new subcommands.		Note that it was only capable of a few subcommands before version 0.1.2 (i.e. versions 0.1.19 and before). However from 1.2 onwards it has many more new subcommands.
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		+	= Brief description of subcommands =
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		+	* '''bcftools query''', extracts fields from VCF or BCF files and outputs them in user-defined format.

	= Usage =		= Usage =

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	= Usage =		= Usage =
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		+	* When using '''samtools mpileup''', the output can be piped to
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		+	bcftools view -cgbu

	The '''bcftools filter''' capability is one of the new tools from bcftools v1.2		The '''bcftools filter''' capability is one of the new tools from bcftools v1.2