What it does

This tool estimates the number of indels for every alignment block of the MAF file.

Note

Any block/s not containing exactly 2 species will be omitted.

Example

• For the following alignment block:

  a score=7233.0
  s hg18.chr1     100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
  s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC----
  

• running this tool will return:

  #Block   Source            Seq1_Start        Seq1_End  Seq2_Start    Seq2_End        Indel_length
  1       hg18.chr1            101              102         202             204              2
  1       rheMac2.chr11        103              104         204             205              1
  1       rheMac2.chr11        129              133         229             230              4