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sv2nl

Table of Contents

Aim

sv2nl is a tool that maps structural variants to non-linear transcripts.

Usage

sv2nl -h will show the help message. Currently, the tool only supports VCF files as input. DNA structural variations are from delly and Non-linear transcripts are from scannls. The output is threes tsv files, one for each type of structural variation (duplication, inversion, translocation). However, You can use the -m option to merge all the output files into one.

$ sv2nl -h
Map structural Variation to Non-Linear Transcription
Usage:
  sv2nl [OPTION...] [sv non-linear]

      --sv arg          The file path of segment information from delly
      --non-linear arg  The file path of non-linear information from scannls
      --dis arg         The distance threshold for trans mapper (default: 1000000)
  -o, --output arg      The file path of output (default: output.tsv)
  -t, --thread arg      The number of thread program use (default: 4)
  -m, --merge           If provided only merge outputs into one file
  -d, --debug           Print debug info
  -h, --help            Print help
  -v, --version         Print the current version number

Example 1

example.sv.vcf is the DNA structural variation file from delly. example.non-linear.vcf is the non-linear transcript. Option -t define the number of threads. Option -o define the output file prefix. If you don't provide -o option, the output file prefix will be output.tsv. You will get three output files (output.tsv.dup , output.tsv.inv, output.tsv.tra). If -m option is provided, you will get one output file (output.tsv).

$ sv2nl example.sv.vcf example.non-linear.vcf -o example.tsv -t 4

Performance

The performance is tested simply by time and heapstack command. It is not a benchmark.

SV File Size SV Records NL File Size NL Records Time Peak Memory Usage
26MB 72'496 2.4MB 10'510 18S 25.66MB

Current Issues