Man pages sections > man1 > findknownsnps

findknownsnps - main executable for snpomatic

FINDKNOWNSNPS(1) SNP-o-matic Manual FINDKNOWNSNPS(1)

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)
SNP-o-matic 1.0