FINDKNOWNSNPS(1)

📦
version 1.0 · 4 versions
, in debian trixie, ubuntu noble, ubuntu questing

✨ FINDKNOWNSNPS — the snpomatic main character ✨

okay bestie, this is section 1 of the SNP-o-matic manual, and we are about to get so acquainted 💖

🌸 NAME 🌸

findknownsnps — the main executable for snpomatic. that's it, that's the whole job. she's the star of the show 👑

🎀 SYNOPSIS 🎀

findknownsnps <options>

🦋 DESCRIPTION 🦋

findknownsnps is the main executable for the snpomatic software. no cap, she's the one you actually run 🫶

💅 OPTIONS 💅

These options control whether output is written to file(s), standard output, or directly to a man pager. pick your fighter ✨

  • --genome=GENOME_FILE — FASTA file with chromosomes. this one is mandatory, bestie, you literally cannot skip it 🚨
  • --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. (yes she's listed twice in the original, and we respect her journey 💀)
  • --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 — this is the read mate 💞
  • --nono=FILENAME — file with a list of read names (!) to ignore. optional. and yes, the (!) is doing a lot of work there, pay attention 👀
  • --regions=REGION_FILE — region file for finding new SNPs. optional. [DEPRECATED] — she's retired, show her some respect but maybe don't build your life around her 🪦
  • --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! and it implies—noshortcuts. optional. iconic, no reads required 💅
  • --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] — she's still in her building era, be gentle 🚧
  • --fragmentplot=FILENAME — outputs a plot of fragment size distribution to a file. optional. we love a data visualization moment 📊
  • --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. it's giving exes at a party 🙈
  • --sqlite=FILENAME — creates a sqlite text file with alignment data. [EXPERIMENTAL] — optional. proceed with the energy of someone reading a beta changelog 🧪
  • --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. the index will be created if it does not exist. optional.
  • --noshortcuts — will process all chromosomal regions, even those with lots’o’repeats. optional; no value. she does NOT take shortcuts, the name is not a bit 🔥
  • --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. strange side effects is doing a LOT of heavy lifting in that sentence, be aware 😭
  • --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.
💖 reminder bestie: every flag, every default, every <red>[DEPRECATED]</red> and <yellow>[EXPERIMENTAL]</yellow> and <yellow>[UNDER CONSTRUCTION]</yellow> tag is here for a reason. don't skip the scary ones. 🫶

and that's the whole page, you ate that 💅✨ this was the SNP-o-matic 1.0 era of the manual, page FINDKNOWNSNPS(1) — go forth and find those known SNPs, queen 👑🧬🌸

📦 where this page comes from