Split parameter setting

[Larrycpan]

I am using CaVEMan in HPC for multiple samples parallelly, and am wondering how to set the parameter -i? In local system, I used -i 1 for testing, but it only output the result of chr1. Thanks for your reply.

[AndyMenzies]

Hi

There is a github wiki page that covers much of this - https://github.com/cancerit/cgpCaVEManWrapper/wiki/Execution

In the split step, -index (-i) refers to the contig line in your genome.fa.fai file. ie if you only use 1, you get chr1. You need to run one job per chromosome you want to process.