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)