Question: calling SV (or CNV) on CANCER SAMPLES with no GERMLINE
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gravatar for Bogdan
2.3 years ago by
Bogdan970
Palo Alto, CA, USA
Bogdan970 wrote:

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

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