from a chromosome indels file delete_overlapping_indels.pl $inputFile1 $inputIndelStartColumnNumber2 $inputIndelEndColumnNumber3 $outputFile1

.. class:: infomark **What it does** This program detects overlapping indels in a chromosome and keeps all non-overlapping indels. As for overlapping indels, the first encountered one is kept and all others are removed. It requires three inputs: - The first input is a TABULAR format file containing coordinates of indels in blocks extracted from multi-alignment. - The second input is an integer number representing the number of the column where indel start coordinates are stored in the input file. - The third input is an integer number representing the number of the column where indel end coordinates are stored in the input file. - The output is a TABULAR format file containing all non-overlapping indels in the input file, and the first encountered indel of overlapping ones. Note: The number of the first column is 1. **Example** Let us have the following insertions in the human genome. The start and end coordinates of insertions are on columns 5 and 6 respectively:: 3 hg18.chr22_insert 3 hg18.chr22 14508610 14508612 3924 - panTro2.chr2b 132518950 132518951 3910 + rheMac2.chr17 14311798 14311799 3896 + 7 hg18.chr22_insert 13 hg18.chr22 14513678 14513690 348 - panTro2.chr2b 132517876 132517877 321 + rheMac2.chr17 14274462 14274463 337 + 7 hg18.chr22_insert 6 hg18.chr22 14513688 14513699 348 - panTro2.chr2b 132517879 132517880 321 + rheMac2.chr17 14274465 14274466 337 + 25 hg18.chr22_insert 9 hg18.chr22 14529501 14529509 385 - panTro2.chr22 14528775 14528776 376 - rheMac2.chr9 42869449 42869450 375 - 36 hg18.chr22_insert 4 hg18.chr22 14566316 14566319 540 - panTro2.chr2b 132492077 132492078 533 + rheMac2.chr10 59230438 59230439 533 - 40 hg18.chr22_insert 7 hg18.chr22 14508610 14508616 2337 - panTro2.chr2b 132487750 132487751 2313 + rheMac2.chr10 59128305 59128306 2332 + 41 hg18.chr22_insert 4 hg18.chr22 14571556 14571559 2483 - panTro2.chr2b 132485878 132485879 2481 + rheMac2.chr10 59126094 59126095 2508 + By removing the overlapping indels which, we get:: 3 hg18.chr22_insert 3 hg18.chr22 14508610 14508612 3924 - panTro2.chr2b 132518950 132518951 3910 + rheMac2.chr17 14311798 14311799 3896 + 7 hg18.chr22_insert 13 hg18.chr22 14513678 14513690 348 - panTro2.chr2b 132517876 132517877 321 + rheMac2.chr17 14274462 14274463 337 + 25 hg18.chr22_insert 9 hg18.chr22 14529501 14529509 385 - panTro2.chr22 14528775 14528776 376 - rheMac2.chr9 42869449 42869450 375 - 36 hg18.chr22_insert 4 hg18.chr22 14566316 14566319 540 - panTro2.chr2b 132492077 132492078 533 + rheMac2.chr10 59230438 59230439 533 - 41 hg18.chr22_insert 4 hg18.chr22 14571556 14571559 2483 - panTro2.chr2b 132485878 132485879 2481 + rheMac2.chr10 59126094 59126095 2508 +