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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

ANNOTATE-OUTPUT(1)					      General Commands Manual						ANNOTATE-OUTPUT(1)

NAME

       annotate-output - annotate program output with time and stream

SYNOPSIS

       annotate-output [options] program [args ...]

DESCRIPTION

       annotate-output will execute the specified program, while prepending every line with the current time and O for stdout and E for stderr.

OPTIONS

       +FORMAT
	      Controls the timestamp format, as per date(1).  Defaults to "%H:%M:%S".

       -h, --help
	      Display a help message and exit successfully.

EXAMPLE

       $ annotate-output make
       21:41:21 I: Started make
       21:41:21 O: gcc -Wall program.c
       21:43:18 E: program.c: Couldn't compile, and took me ages to find out
       21:43:19 E: collect2: ld returned 1 exit status
       21:43:19 E: make: *** [all] Error 1
       21:43:19 I: Finished with exitcode 2

BUGS

       Since  stdout  and  stderr  are	processed  in parallel, it can happen that some lines received on stdout will show up before later-printed
       stderr lines (and vice-versa).

       This is unfortunately very hard to fix with the current annotation strategy.  A fix would involve  switching  to  PTRACE'ing  the  process.
       Giving nice a (much) higher priority over the executed program could however cause this behaviour to show up less frequently.

       The program does not work as well when the output is not linewise.  In particular, when an interactive program asks for input, the question
       might not be shown until after you have answered it.  This will give the impression that the annotated program has hung, while it has not.

SEE ALSO

       date(1)

SUPPORT

       This program is community-supported (meaning: you'll need to fix it yourself).  Patches are however appreciated, as is any feedback  (posi-
       tive or negative).

AUTHOR

       annotate-output	was written by Jeroen van Wolffelaar <jeroen@wolffelaar.nl> This manpage comes under the same copyright as annotate-output
       itself, read /usr/bin/annotate-output (or wherever you install it) for the details.

DEBIAN
								 Debian Utilities						ANNOTATE-OUTPUT(1)
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