xenial (1) findknownsnps.1.gz

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)