for 3-way alignments getIndelRates_3way.py $input1 $out_file1 #if $region.type == "align" "None" #else $region.input2 $input2.dbkey $input2.metadata.chromCol,$input2.metadata.startCol,$input2.metadata.endCol,$input2.metadata.strandCol #end if Intervals in your history Alignment block

.. class:: infomark **What it does** This tool estimates the insertion and deletion rates for alignments in a window of specified size. Rates are computed over the total adjusted lengths (adjusted by disregarding masked bases) of all the alignments blocks from the indel file that fall within that window. ----- .. class:: warningmark **Note** This tool only works on the output of the 'Estimate Indel Rates for 3-way alignments' tool.