calling SV (or CNV) on CANCER SAMPLES with no GERMLINE

Question

[Bogdan]

Dear all,

I would appreciate please a piece of help and advice : when calling SV (or CNV) on TUMOR samples (that do not have GERMLINE counterparts), what strategy would you please advise :

1 -- running a SV caller on a TUMOR sample in a "germline"-mode

2 -- running a SV caller on a TUMOR sample vs a GERMLINE, where the GERMLINE can be any UNMATCHED NORMAL

3 -- running a SV caller on a TUMOR sample vs a GERMLINE, where the GERMLINE can be any COLLECTION of UNMATCHED NORMAL samples (i.e. I could merge the BAM files for many germline samples).

thanks,

bogdan