findknownsnps - Online in the Cloud

PROGRAM:

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)

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