NAME

       gt-hop - Reference-based homopolymer error correction.

SYNOPSIS

       gt hop -<mode> -ref <encseq> -map <sam/bam> -reads <fastq> [options...]

OPTIONS

       -ref
           reference sequence in GtEncseq format (can be prepared using gt encseq encode)

       -map
           mapping of reads to reference it must be in SAM/BAM format, and sorted by coordinate (can be prepared
           e.g. using: samtools sort)

       -sam
           mapping file is SAM (default: BAM)

       -aggressive
           correct as much as possible

       -moderate
           mediate between sensitivity and precision

       -conservative
           correct only most likely errors

       -expert
           manually select correction criteria

       -reads
           uncorrected read file(s) in FastQ format; the corrected reads are output in the currect working
           directory in files which are named as the input files, each prepended by a prefix (see -outprefix
           option) -reads allows one to output the reads in the same order as in the input and is mandatory if
           the SAM contains more than a single primary alignment for each read (e.g. output of bwasw) see also
           -o option as an alternative

       -outprefix
           prefix for output filenames (corrected reads)when -reads is specified the prefix is prepended to each
           input filename (default: hop_)

       -o
           output file for corrected reads (see also -reads/-outprefix) if -o is used, reads are output in a
           single file in the order they are found in the SAM file (which usually differ from the original
           order) this will only work if the reads were aligned with a software which only includes 1 alignment
           for each read (e.g. bwa) (default: undefined)

       -v
           be verbose (default: no)

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

DESCRIPTION

       Correction mode:

       One of the options -aggressive, -moderate, -conservative or -expert must be selected.

       The -aggressive, -moderate and -conservative modes are presets of the criteria by which it is decided if
       an observed discrepancy in homopolymer length between reference and a read shall be corrected or not. A
       description of the single criteria is provided by using the -help+ option. The presets are equivalent to
       the following settings:

                               -aggressive    -moderate      -conservative
           -hmin               3              3              3
           -read-hmin          1              1              2
           -altmax             1.00           0.99           0.80
           -refmin             0.00           0.00           0.10
           -mapqmin            0              10             21
           -covmin             1              1              1
           -clenmax            unlimited      unlimited      unlimited
           -allow-multiple     yes            yes            no

       The aggressive mode tries to maximize the sensitivity, the conservative mode to minimize the false
       positives. An even more conservative set of corrections can be achieved using the -ann option (see
       -help+).

       The -expert mode allows one to manually set each parameter; the default values are the same as in the
       -conservative mode.

       (Finally, for evaluation purposes only, the -state-of-truth mode can be used: this mode assumes that the
       target sequence of the sequencing has been specified as reference sequence and outputs an ideal list of
       corrections.)

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                                   10/10/2012                                          GT-HOP(1)