Bcftools

The canonical samtools follower

: GATK

suggests : VCFtools

---

[ BioWare | Main_Page ]

---

bcftools (HTSlib).

Note: A fast HTSlib C version of a filtering tool is now available (see bcftools filter and bcftools view).

Tool page: http://vcftools.sourceforge.net/htslib.html

bcftools
 
Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: 0.2.0-rc6-37-g17d49cf (using htslib 0.2.0-rc6-32-g20df6b9)
 
Usage:   bcftools <command> <argument>
 
Commands:
 
 -- Indexing:
	index           index VCF/BCF files
 
 -- Core VCF/BCF tools:
	annotate        annotate and edit VCF/BCF files
	call            SNP/indel calling (former "view")
	filter          filter VCF/BCF files using fixed thresholds
	gtcheck         check sample concordance, detect sample swaps and contamination
	isec            intersections of VCF/BCF files
	merge           merge VCF/BCF files (one-sample files yield multi-sample file)
	norm            left-align normalize indels
	query           transform VCF/BCF into user-defined formats
	stats           produce VCF/BCF stats (former vcfcheck)
	view            VCF/BCF conversion, view, subset and filter VCF/BCF files
 
 -- Other/Experimental tools:
	roh             identify runs of autozygosity (HMM)
	som             filter using Self-Organized Maps (experimental)
 
Notes:  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.

---

References:

---

[ BioWare | Main_Page ]