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)