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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'



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