Some of the originalįunctionality has been temporarily lost in the process of transition to htslib,īut will be added back on popular demand. This command replaces the former "bcftools view" caller. To be used in conjunction with samtools mpileup. See man page for detailsįormerly known as bcftools view, this is the successor of the popular caller from the samtools package with extended capabilities.Ībout: SNP/indel variant calling from VCF/BCF. R, -remove list of annotations to remove (e.g. r, -regions restrict to comma-separated list of regions or regions listed in a file, see man page for details p, -plugins comma-separated list of dynamically loaded user-defined plugins. O, -output-type b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF See BCFTOOLS_PLUGINS environment variable and man page for details l, -list-plugins list available plugins. h, -header-lines lines which should be appended to the VCF header c, -columns list of columns in the annotation file, e.g. a, -annotations VCF file or tabix-indexed file with annotations: CHR\tPOS+ Git clone git:///samtools/bcftools.git bcftoolsĪdds or removes annotations, support for user-written plugins. Git clone git:///samtools/htslib.git htslib
Bcftools manual software#
The software is under heavyĭevelopment and the option -branch may be required. Page for the up-to-date version of the clone command. The clone command is run only once, the pullĬommand is run whenever the latest snapshots from github is needed. It can be downloaded and compiled the usual way. It is designed for speed and works with both VCF and
Please visit the new website here: /htslib.html The bcftools/htslib VCF commands As of July 2015, the VCFtools project has been moved to github!
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