Syntax

This tool converts a LAV formated file to the BED format.

• LAV format LAV is an alignment format developed by Webb Miller's group at Penn State University. It is the primary output format for BLASTZ.
• BED format Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser.

Example

• Convert LAV format:

  #:lav
  s {
    "/depot/data2/galaxy/hg16/seq/chr19.nib" 1 63811651 0 1
    "/depot/data2/galaxy/mm5/seq/chr11.nib" 1 121648857 0 1
  }
  h {
    "> hg16.chr19"
    "> mm5.chr11 (reverse complement)"
  }
  a {
    s 3500
    b 3001012 70568380
    e 3001075 70568443
    l 3001012 70568380 3001075 70568443 81
  }
  a {
    s 3900
    b 3008279 70573976
    e 3008357 70574054
    l 3008279 70573976 3008357 70574054 78
  }
  #:eof
  

• To two BED formated files:

  chr19       3001011 3001075 hg16_0  0       +
  chr19       3008278 3008357 hg16_1  0       +
  

and:

chr11       70568379        70568443        mm5_0   0       +
chr11       70573975        70574054        mm5_1   0       +