findknownsnps1

Usage

Overview

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)