bcftools

Software Summary

Mesabi

Default Module: 

1.16-gcc-8.2.0-5d4xg4y

Other Modules Available: 

1.16-gcc-8.2.0-5d4xg4y, 1.10.2, 1.9, 0.2.0, 1.2, 1.6

Last Updated On: 

Tuesday, November 14, 2023

Mesabi K40

Default Module: 
Other Modules Available: 
Last Updated On: 

Mangi

Default Module: 
1.16-gcc-8.2.0-5d4xg4y
Other Modules Available: 

1.16-gcc-8.2.0-5d4xg4y, 1.10.2, 1.9, 0.2.0, 1.2, 1.6

Last Updated On: 

Tuesday, November 14, 2023

Mangi v100

Default Module: 
Other Modules Available: 
Last Updated On: 

NICE

Default Module: 
Other Versions Available: 
Last Updated On: 
Last Updated On: 

Tuesday, November 14, 2023

Support Level: 
Primary Support
Software Access Level: 
Open Access
Software Categories: 
Genetics
Software Description

BCFtools are meant as a faster replacement for most of the perl VCFTools commands.

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.

Bcftools is designed to work on a stream. It regards an input file "-" as the standard input (stdin) and outputs to the standard output (stdout). Several commands can thus be combined with Unix pipes.

 

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