--- name: "gt-hop" section: "1" platform: "linux" package: "genometools" version: "1.6.5+ds-2.2" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/gt-hop" --- # gt-hop(1) Cognate sequence-based homopolymer error correction. ## NAME gt-hop - Cognate sequence-based homopolymer error correction. ## SYNOPSIS **gt hop** -\ -c \ -map \ -reads \ \[options...\] ## DESCRIPTION - **-c** \[*string*\] cognate sequence (encoded using gt encseq encode) - **-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) - **-sam** \[*yes\|no*\] mapping file is SAM default: BAM - **-aggressive** \[*yes\|no*\] correct as much as possible - **-moderate** \[*yes\|no*\] mediate between sensitivity and precision - **-conservative** \[*yes\|no*\] correct only most likely errors - **-expert** \[*yes\|no*\] 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** \[*string*\] 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 - **-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 - **-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 ``` 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 sequenced genome has been specified as cognate sequence and outputs an ideal list of corrections.) ## REPORTING BUGS Report bugs to https://github.com/genometools/genometools/issues.