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)

                                          December 2015                          FINDKNOWNSNPS(1)