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GT-HOP(1) | GenomeTools Manual | GT-HOP(1) |
NAME¶
gt-hop - Cognate sequence-based homopolymer error correction.SYNOPSIS¶
gt hop -<mode> -c <encseq> -map <sam/bam> -reads <fastq> [options...]DESCRIPTION¶
-c [string]cognate sequence (encoded using gt encseq encode)
(default: undefined)
-map [string]
mapping of reads to the cognate sequence it must be in
SAM/BAM format, and sorted by coordinate (can be prepared e.g. using: samtools
sort) (default: undefined)
-sam [yes|no]
mapping file is SAM default: BAM (default: no)
-aggressive [yes|no]
correct as much as possible (default: no)
-moderate [yes|no]
mediate between sensitivity and precision (default:
no)
-conservative [yes|no]
correct only most likely errors (default: no)
-expert [yes|no]
manually select correction criteria (default: no)
-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 [string]
prefix for output filenames (corrected reads)when -reads
is specified the prefix is prepended to each input filename (default:
hop_)
-o [string]
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)
-hmin [value]
minimal homopolymer length in cognate sequence (default:
3)
-read-hmin [value]
minimal homopolymer length in reads (default: 2)
-qmax [value]
maximal average quality of homopolymer in a read
(default: 120)
-altmax [value]
max support of alternate homopol. length; e.g. 0.8 means:
do not correct any read if homop. length in more than 80% of the reads has the
same value, different from the cognate if altmax is set to 1.0 reads are
always corrected (default: 0.800000)
-cogmin [value]
min support of cognate sequence homopol. length; e.g. 0.1
means: do not correct any read if cognate homop. length is not present in at
least 10% of the reads if cogmin is set to 0.0 reads are always corrected
(default: 0.100000)
-mapqmin [value]
minimal mapping quality (default: 21)
-covmin [value]
minimal coverage; e.g. 5 means: do not correct any read
if coverage (number of reads mapped over whole homopolymer) is less than 5 if
covmin is set to 1 reads are always corrected (default: 1)
-allow-muliple [yes|no]
allow multiple corrections in a read (default: no)
-clenmax [value]
maximal correction length default: unlimited (default:
undefined)
-ann [string]
annotation of cognate sequence it must be sorted by
coordinates on the cognate sequence (this can be e.g. done using: gt gff3
-sort) if -ann is used, corrections will be limited to homopolymers startingor
ending inside the feature type indicated by -ft optionformat: sorted GFF3
(default: undefined)
-ft [string]
feature type to use when -ann option is specified
(default: CDS)
-v [yes|no]
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
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 cognate sequence 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
REPORTING BUGS¶
Report bugs to <gt-users@genometools.org>.09/05/2014 | GenomeTools 1.5.3 |