svgen

generate DNA Structural Variation from FASTA format (Node.js)

Overview

Installation

npm install svgen

Usage

command line

# get information sv and snp randomly generated.
svbedgen sample.fasta > sv.bed

# get fasta with SV and SNP designated in a bed file
svgen sv.bed sample.fasta  > chr11_sv.fasta

# get converted coordinates caused by SVs
svcoordinate sample.fasta sv.bed coordinate.bed > new_coordinate.bed

**** svbedgen ****
[synopsis]
  svbedgen <fasta file>
[options]
  ** length: the lengths of SVs.
  --svlen <int> mean length of SVs. default:1500
  --inslen <int>  mean length of insertions. default: the same as "svlen" option. if 0, then no insertions are registered.
  --dellen <int>  mean length of deletions. default: the same as "svlen" option. if 0, then no deletions are registered.
  --invlen <int>  mean length of inversions. default: the same as "svlen" option. if 0, then no inversions are registered.
  --duplen <int>  mean length of tandem duplications. default: the same as "svlen" option. if 0, then no tandem duplications are registered.
  --tralen <int>  mean length of translocations. default: the same as "svlen" option. if 0, then no translocations are registered.

  ** deviation : standard deviation of each SVs.
  --svdev <int> stddev of SVs. default:300
  --insdev <int>  stddev of insertions. default: the same as "svlen" option
  --deldev <int>  stddev of deletions. default: the same as "svlen" option
  --invdev <int>  stddev of inversions. default: the same as "svlen" option
  --dupdev <int>  stddev of tandem duplications. default: the same as "svdev" option.
  --tradev <int>  stddev of translocations. default: the same as "svlen" option

  ** number: total number of SVs.
  --sv <int>  the number of SVs to register. default:10000. If each SV is specifically designated its number, that configuration priors to this.

  ** rate : the rate of each SV type, determined by the following rule.
  *  let "total" be the sum of each num, i.e. insnum, delnum, invnum, dupnum and tranum.
  *  the rate of each SV is  x / total, where x is one of insnum, delnum, invnum, dupnum or tranum.
  --insnum <int>  for insertions. default: 200.
  --delnum <int>  for deletions. default: 200.
  --invnum <int>  for inversions. default: 200.
  --dupnum <int>  for tandem duplications. default: 200.
  --tranum <int>  for translocations. default: 200.

  ** repeat number of tandem duplication.
  --duprep <int>  mean repeat folds of tandem duplications. default: 40.
  --duprdev <int> stddev of repeat folds of tandem duplications. default: 10.

  ** configuration for SNP.
  * for simplicity, only single nucleotide alteration is supported.
  --snprate reciprocal rate to insert SNP default:10000 (1/10000). if 0, then no SNPs are registered.

  ** configuration for a fasta file.
  --rnames <sequence id1>[,sequence_id2,...]   sequence ids to use. default: null (use all rnames in a fasta file.)
  --json <json file>   fasta summary file to shortcut calculation.

**** svgen ****
[usage]
  svgen <bed file> <fasta file>
[options]
  --rnames|-r <sequence id1>[,sequence_id2,...]   sequence ids to use. default: null (use all rnames in a fasta file.)
  --json|-j <json file>  fasta summary file to shortcut calculation.
[bed file columns]
  rname start-position  end-position  SVtype(DEL|INS|INV|DUP|TRA|SNP) length  extra-info

**** svcoordinate ****
[usage]
  svcoordinate <fasta file> <sv bed file> <coordinate bed file>
[options]
  --nosort : not using sort toward coordinate bed file
  --verbose|-v: verbose logging