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