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vcf-annotate(1) [debian man page]

VCF-ANNOTATE(1) 						   User Commands						   VCF-ANNOTATE(1)

NAME

       vcf-annotate - annotate VCF file, add filters or custom annotations

SYNOPSIS

       cat in.vcf | vcf-annotate [OPTIONS] > out.vcf

DESCRIPTION

       About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.

	      Currently annotates only the INFO column, but it will be extended on demand.

OPTIONS

       -a, --annotations <file.gz>
	      The tabix indexed file with the annotations: CHR	FROM[	TO][	VALUE]+.

       -c, --columns <list>
	      The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third
	      column should be ignored. If TO is not present, it is assumed that TO equals to FROM.

       -d, --description <file|string>
	      Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'.  The descriptions can be  read  from  a
	      file, one annotation per line.

       -f, --filter <list>
	      Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.

       -h, -?, --help
	      This help message.

   Filters:
       +      Apply all filters with default values (can be overridden, see the example below).

       -X     Exclude the filter X

       1, StrandBias
	      FLOAT		       Min P-value for strand bias (given PV4) [0.0001]

       2, BaseQualBias
	      FLOAT		     Min P-value for baseQ bias [1e-100]

       3, MapQualBias
	      FLOAT		      Min P-value for mapQ bias [0]

       4, EndDistBias
	      FLOAT		      Min P-value for end distance bias [0.0001]

       a, MinAB
	      INT			    Minimum number of alternate bases [2]

       c, SnpCluster
	      INT1,INT2 	       Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []

       D, MaxDP
	      INT			    Maximum read depth [10000000]

       d, MinDP
	      INT			    Minimum read depth [2]

       q, MinMQ
	      INT			    Minimum RMS mapping quality for SNPs [10]

       Q, Qual
	      INT			     Minimum value of the QUAL field [10]

       r, RefN
	      Reference base is N []

       W, GapWin
	      INT			   Window size for filtering adjacent gaps [10]

       w, SnpGap
	      INT			   SNP within INT bp around a gap to be filtered [10]

   Example:
	      zcat  in.vcf.gz  |  vcf-annotate	-a  annotations.gz  -d	descriptions.txt  |  bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f
	      +/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz

   Where descriptions.txt contains:
	      key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'

vcf-annotate 0.1.5						     July 2011							   VCF-ANNOTATE(1)

Check Out this Related Man Page

HWLOC-ANNOTATE(1)						       hwloc							 HWLOC-ANNOTATE(1)

NAME

       hwloc-annotate - Add info attributes to a XML topology

SYNOPSIS

       hwloc-annotate [options] <input.xml> <output.xml> <location> <mode> <annotation>

OPTIONS

       --ci	 Clear the existing info attributes in the target objects before annotating.  If no new annotation has to be added after clearing,
		 mode should be set to none.

DESCRIPTION

       hwloc-annotate loads a topology from a XML file, adds some annotations, and export the resulting topology to another XML file.	The  input
       and output files may be the same.  The annotation may be string info attributes.  This is specified by the mode:

       info <name> <value>
	      Specifies a new string info attribute whose name is name and value is value.

       none   No new annotation is added. This is useful when clearing existing attributes.

       Annotations may be added to one specific object in the topology, all of them, or all of a given type.  This is specified by the location:

       all    annotates all objects in the topology.

       root   annotates the root object of the topology.

       <type>:all
	      annotates all objects of the given type.

       <type>:<index>
	      annotates the object of the given type and index.  The index is logical.

       NOTE: The existing annotations may be listed with hwloc-info.

       NOTE:  It  is  highly recommended that you read the hwloc(7) overview page before reading this man page.  Most of the concepts described in
       hwloc(7) directly apply to the hwloc-annotate utility.

EXAMPLES

       hwloc-annotate's operation is best described through several examples.

       Add an info attribute to all Core objects:

	   $ hwloc-annotate input.xml output.xml Core:all infoname infovalue

       Add an info attribute to the root object of the topology and modify the input XML directly:

	   $ hwloc-annotate file.xml file.xml root infoname infovalue

RETURN VALUE

       Upon successful execution, hwloc-annotate generates the output topology.  The return value is 0.

       hwloc-annotate will return nonzero if any kind of error occurs, such as (but not limited to) failure to parse the command line.

SEE ALSO

       hwloc(7), lstopo(1), hwloc-info(1)

1.7								   Apr 07, 2013 						 HWLOC-ANNOTATE(1)
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