for combining indel interval data indel_table.py --input1=$input1 --sum1=$sum1 --input2=$input2 --sum2=$sum2 --output=$output1 #for $i in $inputs ${i.input} ${i.sum} #end for

**What it does** Creates a table allowing for analysis and comparison of indel data. Combines any number of interval files that have been produced by the tool that converts indel SAM data to interval format. Includes overall total counts for all or some files. The tool has the option to not include a given file's counts in the total column. This could be useful for combined data if the counts for certain indels might be included more than once. The exact columns of the output will depend on the columns of the input. Here is the detailed specification of the output columns:: Column Description ------------------------------- ---------------------------------------------------------------------------------- 1 ... m "Indel" All the "indel" columns, which contain the info that will be checked for equality m + 1 Total Occurrences Total number of occurrences of this indel across all (included) files m + 2 Occurrences for File 1 Number of occurrences of this indel for first file m + 3 Occurrences for File 2 Number of occurrences of this indel for second file [m + ...] [...] [Number of occurrences of this indel for ... file] The most likely columns would be from the output of the Convert SAM to Interval/BED tool, so: Chromosome, Start position, End position, I/D (Insertion/Deletion), -/<base(s)> (Deletion/Inserted base(s)), Total Occurrences (across files), Occurrences for File 1, Occurrences for File 2, etc. See below for an example. ----- **Example** Suppose you have the following 4 files:: chrM 300 301 D - 6 chrM 303 304 D - 19 chrM 359 360 D - 1 chrM 410 411 D - 1 chrM 435 436 D - 1 chrM 410 411 D - 1 chrM 714 715 D - 1 chrM 995 997 D - 1 chrM 1168 1169 I A 1 chrM 1296 1297 D - 1 chrM 300 301 D - 8 chrM 525 526 D - 1 chrM 958 959 D - 1 chrM 995 996 D - 3 chrM 1168 1169 I C 1 chrM 1296 1297 D - 1 chrM 303 304 D - 22 chrM 410 411 D - 1 chrM 435 436 D - 1 chrM 714 715 D - 1 chrM 753 754 I A 1 chrM 1168 1169 I A 1 and the fifth file:: chrM 303 304 D - 22 chrM 410 411 D - 2 chrM 435 436 D - 1 chrM 714 715 D - 2 chrM 753 754 I A 1 chrM 995 997 D - 1 chrM 1168 1169 I A 2 chrM 1296 1297 D - 1 The following will be produced if you include the first four files in the sum, but not the fifth:: chrM 300 301 D - 14 6 0 8 0 0 chrM 303 304 D - 41 19 0 0 22 22 chrM 359 360 D - 1 1 0 0 0 0 chrM 410 411 D - 3 1 1 0 1 2 chrM 435 436 D - 2 1 0 0 1 2 chrM 525 526 D - 1 0 0 1 0 0 chrM 714 715 D - 2 0 1 0 1 2 chrM 753 754 I A 1 0 0 0 1 1 chrM 958 959 D - 1 0 0 1 0 0 chrM 995 996 D - 3 0 0 3 0 0 chrM 995 997 D - 1 0 1 0 0 1 chrM 1168 1169 I A 2 0 1 0 1 2 chrM 1168 1169 I C 1 0 0 1 0 0 chrM 1296 1297 D - 2 0 1 1 0 1 The first numeric column includes the total or the next four columns, but not the fifth.