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\tFROM[\tTO][\tVALUE]+.

       -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'