---
name: "findknownsnps"
section: "1"
platform: "linux"
package: "snpomatic"
version: "1.0-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/findknownsnps"
---

# findknownsnps(1)

main executable for snpomatic

## 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)