Apparently, I did not read through the manual carefully.
somatic_sv.pl has some parameters that provide information for normal genome.
I am trying to identify somatic structural variations with WES from paired normal and tumor samples by using the software Meerkat. http://compbio.med.harvard.edu/Meerkat/
(1) I read through their manual, but cannot figure out how "somatic" is decided. My understanding is that the software pipleline runs on paired normal sample and tumor sample respectively with slightly different parameter settings and get 2 lists of structural variations. Somatic structural variations are decided by comparing these 2 lists, and this part is not included in the software. I am worrying that the list from tumor would not include all or at least the most of variations in the list from normal. Does any one have any experience with this software? How should I proceed to get somatic structural variations for paired samples?
(2) Could any one please give me the link to download repeat mask file? -R STR /path/to/repeat_mask_file, required, can be downloaded from UCSC