(4) To split a genome-wide analysis into non-overlapping chunks and to run each on a distinct CPU core, FastQTL includes a set of user-friendly options. It can either split the data into a given number of chunk (--chunk 12 200 to run chunk 12 out of 200) or focus on a particular user defined genomic region (--region 20:1-1000000). The phenotype and genotype data included in the genomic region is then automatically extracted from the cis-window size and analyzed. A simple loop going through all possible chunks allows the user to submit the full analysis on a compute cluster or server. A FastQTL example command line to perform a genome-wide analysis is shown in command 1.
