Joint segmentation in sequenza

[rkendar]

Hi Francesco,

Is it possible to do joint segmentation in sequenza? This because I am working on multi-sectors tumor sample, meaning that I have 1 normal and 3 tumor samples from the same patients.

Based on what I understand from manual, I can can change the seg.alg option to aspcf or pcf in sequenza.extract. I also checked copynumber manual on

https://bioconductor.org/packages/release/bioc/manuals/copynumber/man/copynumber.pdf . 

My questions is:

1. So to perform joint segmentation I have to use "aspc" instead of "pcf", is it correct? 

2. Do you have "multipfc" also in seg.alg options for joint segmentation?

3. Can the bam2seqz take more than 1 tumor .bam?

Thank you,

R