.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH TTUNER "1" "October 2018" "ttuner 3.0.6~beta" "User Commands"
.SH NAME
ttuner \- interpretation of DNA Sanger sequencing data
.SH DESCRIPTION
.TP
\fB\-h\fR
(Help) This message
.TP
\fB\-Q\fR
(Quiet) Turn off status messages
.TP
\fB\-V\fR
(Verbose) Output more status messages
.TP
\fB\-nocall\fR
Disable base recalling and just use the original
called bases read from the input sample file
.TP
\fB\-recalln\fR
Disable adding bases to or deleting from the
original called sequence. Only recall Ns
.TP
\fB\-het\fR
Call call hetezygotes
.TP
\fB\-mix\fR
Call mixed bases
.TP
\fB\-min_ratio\fR <ratio>
Override the default threshold ratio of heights of
.TP
\fB\-trim_window\fR <size>
Set the trimming window size for averaging quality
to the specified value. The default is 10.
.HP
\fB\-trim_threshold\fR <qv> Set the average quality value used in trimming to
.TP
\fB\-C\fR <consensusfile>
Specify the name of the FASTA file which contains
the consensus sequence
.TP
\fB\-edited_bases\fR
Start base recalling from the ABI's edited bases
.TP
\fB\-t\fR <table>
Use specified lookup table. This option overrides
the default (automatic choice of the lookup table)
as well as the options \fB\-3700pop5\fR, \fB\-3700pop6\fR, \fB\-3100\fR,
and \fB\-mbace\fR. To get a message showing
which table was used, specify \fB\-V\fR option
.TP
\fB\-3730\fR
Use the built\-in ABI 3730\-pop7 lookup table
.TP
\fB\-3700pop5\fR
Use the built\-in ABI 3700\-pop5 lookup table
.TP
\fB\-3700pop6\fR
Use the built\-in ABI 3700\-pop6 lookup table
.TP
\fB\-3100\fR
Use the built\-in ABI 3100\-pop6 lookup table
.TP
\fB\-mbace\fR
Use the built\-in MegaBACE lookup table
.TP
\fB\-c\fR
Output SCF file(s), in the current directory
.TP
\fB\-cd\fR <dir>
Output SCF file(s), in the specified directory
.TP
\fB\-cv3\fR
Use version 3 for output SCF file. Default is
version 2.
.TP
\fB\-o\fR <dir>
Output multi\-fasta files of bases (tt.seq),
their locations (tt.pos), quality values (tt.qual)
and status reports (tt.status) to directory <dir>
.TP
\fB\-p\fR
Output .phd.1 file(s), in the current directory
.TP
\fB\-pd\fR <dir>
Output .phd.1 file(s), in the specified directory
.TP
\fB\-q\fR
Output .qual file(s), in the current directory
.TP
\fB\-qa\fR <file>
Append .qual file(s) to <file>
.TP
\fB\-qd\fR <dir>
Output .qual file(s), in the specified directory
.TP
\fB\-s\fR
Output .seq file(s) in FASTA format, in the current
directory
.TP
\fB\-sa\fR <file>
Append .seq file(s) in FASTA format to <file>
.TP
\fB\-sd\fR <dir>
Output .seq file(s) in FASTA format, in the specified
directory
.TP
\fB\-qr\fR <file>
Output a quality report that gives data for a
histogram on the number of reads with quality
values >= 20, to the specified file
.TP
\fB\-if\fR <file>
Read the input sample filenames from the specified
file
.TP
\fB\-id\fR <dir>
Read the input sample files from specified directory
.TP
\fB\-tab\fR
Call heterozygotes or mixed bases and output .tab
file(s) in the  current directory
.TP
\fB\-tabd\fR <dir>
Call mixed bases and output .tab file(s), in the
specified directory
.TP
\fB\-tal\fR
Output .tal file(s),in the current directory
.TP
\fB\-tald\fR <dir>
Output .tal file(s),in the specified directory
.TP
\fB\-hpr\fR
Output a homopolymer runs file in current directory
.TP
\fB\-hprd\fR <dir>
Output a homopolymer runs file(s),in the specified directory
.TP
\fB\-d\fR
Output .poly file(s),in the current directory
.TP
\fB\-dd\fR
<dir>           Output .poly file(s),in the specified directory
.TP
\fB\-ipd\fR <dir>
Input the original bases and peak locations from a
\&.phd file in the specified directory.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.