GT-HOP(1)

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>.