'\" t
.\"     Title: findknownsnps
.\"    Author: [see the "AUTHORS" section]
.\" Generator: Asciidoctor 1.5.4
.\"      Date: 
.\"    Manual: SNP-o-matic Manual
.\"    Source: SNP-o-matic 1.0
.\"  Language: English
.\"
.TH "FINDKNOWNSNPS" "1" "" "SNP\-o\-matic 1.0" "SNP\-o\-matic Manual"
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.SH "NAME"
findknownsnps \- main executable for snpomatic
.SH "SYNOPSIS"
.sp
\fBfindknownsnps\fP <options>
.SH "DESCRIPTION"
.sp
findknownsnps is the main executable for the \fBsnpomatic\fP software.
.SH "OPTIONS"
.sp
These options control whether output is written to file(s), standard output, or
directly to a man pager.
.sp
\fB\-\-genome=GENOME_FILE\fP
.RS 4
FASTA file with chromosomes (mandatory)
.RE
.sp
\fB\-\-fasta=FASTA_FILE\fP
.RS 4
FASTA file with Solexa reads (mandatory, except when \-\-fastq or \-\-index is
used)
.RE
.sp
\fB\-\-fasta=FASTA_FILE\fP
.RS 4
FASTA file with Solexa reads (mandatory, except when \-\-fastq or \-\-index is
used)
.RE
.sp
\fB\-\-fastq=FASTQ_FILE\fP
.RS 4
FASTQ file with Solexa reads (mandatory, except when \-\-fasta or \-\-index is
used)
.RE
.sp
\fB\-\-fastq2=FASTQ_FILE2\fP
.RS 4
FASTQ file with Solexa reads (optional; read mate)
.RE
.sp
\fB\-\-nono=FILENAME\fP
.RS 4
File with list of read names (!) to ignore (optional)
.RE
.sp
\fB\-\-regions=REGION_FILE\fP
.RS 4
Region file for finding new SNPs (optional) [DEPRECATED]
.RE
.sp
\fB\-\-snps=SNP_FILE\fP
.RS 4
Simple SNP file (optional)
.RE
.sp
\fB\-\-gff=GFF_FILE\fP
.RS 4
GFF file with SNPs (optional)
.RE
.sp
\fB\-\-uniqueness=FILE\fP
.RS 4
Output a uniqueness data file for the reference; no Solexa reads needed;
implies\(emnoshortcuts` (optional)
.RE
.sp
\fB\-\-pileup=FILE\fP
.RS 4
Outputs complete pileup into that file (optional)
.RE
.sp
\fB\-\-cigar=FILE\fP
.RS 4
Outputs alignment in CIGAR format (optional)
.RE
.sp
\fB\-\-gffout=FILE\fP
.RS 4
Outputs reads in GFF format (optional)
.RE
.sp
\fB\-\-coverage=FILENAME\fP
.RS 4
Outputs (high depth) coverage data (optional)
.RE
.sp
\fB\-\-wobble=FILENAME\fP
.RS 4
Outputs a list of possible variations (optional; paired reads only)
[UNDER CONSTRUCTION]
.RE
.sp
\fB\-\-fragmentplot=FILENAME\fP
.RS 4
Outputs a plot of fragment size distribution to a file (optional)
.RE
.sp
\fB\-\-snpsinreads=FILENAME\fP
.RS 4
Outputs a list of reads containing known SNPs to a file (optional)
.RE
.sp
\fB\-\-indelplot=FILENAME\fP
.RS 4
Outputs indel data to a file (optional)
.RE
.sp
\fB\-\-inversions=FILENAME\fP
.RS 4
For paired reads, writes read matches indicating inversions into a file (optional)
.RE
.sp
\fB\-\-faceaway=FILENAME\fP
.RS 4
For paired reads, writes read matches that "face away" from each other into a file (optional)
.RE
.sp
\fB\-\-sqlite=FILENAME\fP
.RS 4
Creates a sqlite text file with alignment data [EXPERIMENTAL] (optional)
.RE
.sp
\fB\-\-sam=FILENAME\fP
.RS 4
Creates a SAM alignment file (optional)
.RE
.sp
\fB\-\-spancontigs=FILENAME\fP
.RS 4
Outputs read pairs where "half" reads map uniquely to different
contigs (optional)
.RE
.sp
\fB\-\-bins=FILE_PREFIX\fP
.RS 4
Outputs no\-match, single\-match and multi\-match Solexa reads into prefixed
files (optional)
.RE
.sp
\fB\-\-binmask=MASK\fP
.RS 4
Mask of 1s and 0s to turn off individual bins. Order: No match, single
match, multi\-match, IUPAC. Example: 0100 creates only single\-match bin.
(optional; default:1111)
.RE
.sp
\fB\-\-pair=NUMBER\fP
.RS 4
For paired reads, the length of the first part of the read (mandatory for
paired reads)
.RE
.sp
\fB\-\-fragment=NUMBER\fP
.RS 4
For paired reads, the average fragment length (mandatory for paired reads)
.RE
.sp
\fB\-\-variance=NUMBER\fP
.RS 4
For paired reads, the variance of the fragment length to either side (optional; default: 1/4 of fragment size)
.RE
.sp
\fB\-\-wobblemax=NUMBER\fP
.RS 4
Maximum number of mismatches for wobble (optional; default 2; see \-\-wobble)
.RE
.sp
\fB\-\-mspi=NUMBER\fP
.RS 4
Maximum number of SNPs per chromosomal index (optional; default:8)
.RE
.sp
\fB\-\-index=FILENAME\fP
.RS 4
Index filename (index will be created if it does not exist; optional)
.RE
.sp
\fB\-\-noshortcuts\fP
.RS 4
Will process all chrososomal regions, even those with lots\(cqo\(cqrepeats (optional;
no value)
.RE
.sp
\fB\-\-snpsonly\fP
.RS 4
Only lists found SNPs in the pileup (optional; no value)
.RE
.sp
\fB\-\-chromosome=NAME\fP
.RS 4
Discards all chromosomes but NAME prior to run (optional)
.RE
.sp
\fB\-\-index_from=NUMBER\fP
.RS 4
Starts indexing at this position on all chromosomes (optional)
.RE
.sp
\fB\-\-index_to=NUMBER\fP
.RS 4
Stops indexing at this position on all chromosomes (optional)
.RE
.sp
\fB\-\-chop=NUMBER\fP
.RS 4
 For paired reads, if one but not the other matches, shorten the other by
NUMBER` bases (optional)
.RE
.sp
\fB\-\-index1=NUMBER`\fP
.RS 4
Length of internal index 1 (optional; default:10)
.RE
.sp
\fB\-\-index2=NUMBER\fP
.RS 4
Length of internal index 2 (optional; default:16)
.RE
.sp
\fB\-\-memory_save=NUMBER\fP
.RS 4
Indexes the genome every NUMBER of positions; saves memory and runtime, but
can have strange side effects (optional)
.RE
.sp
\fB\-\-multimatch\fP
.RS 4
Puts a multiple\-matching read to a random position (optional) [currently
paired reads only]
.RE
.sp
\fB\-\-singlematch\fP
.RS 4
Only performs additional output functions for single matches (optional)
[currently paired reads only]
.RE
.sp
\fB\-\-foum\fP
.RS 4
For paired reads, at least one read has to match uniquely in the genome
(force one unique match) (optional)
.RE
.sp
\fB\-\-mismatch\fP
.RS 4
The number of mismatches allowed outside the index (index1+index2)
(optional)
.RE
.sp
\fB\-\-rpa=FILENAME\fP
.RS 4
Writes all read pair alignments into a file (optional)
.RE