Avramopoulos Lab - Free Tools

SumNPL script [download sumnpl.pl]

Use syntax: perl sumnpl.pl scan_data test_locations number_of_picks output_file

The Perl language can be downloaded here

» scan_data is the first input file and the structure of the file has three columns: 1. chromosome number; 2. location [in centimorgans] and 3. NPL score (TAB delimited)

Chromosome	location[cm]	NPL score
1 1 1 1 2 2 .... 22	0 2.5 10.45 22.5 0 4.35 ... 0	-1.3 2.1 0.4 3.1 1.2 -1.7 ... -1.3

» test_locations is the second input file and the structure is similar with the first input file but without the NPL scores (TAB delimited)

Chromosome	location[cm]
1 2 5	32.5 61 13

» number_of_picks is the third parameter and it represents the number of random picks to be compared with the average score for the locations from the second input file
» output_file this is the name of the file in which the results of the analysis will be stored

Avramopoulos lab free tools

SumNPL script [download sumnpl.pl]