Dear All,
I would like to know is there a possibility to asses the significance of CNVs which are obtained as output by ADtex. I was few normal/tumor matched exome data and I applied both Control-FREEC nad ADTex to obtain the CNVs for my data. As for FREEC there is a way to asses significance to the CNVs retrieved to streamline it down to more potential signifianct hits, however is there any such thing possible with ADtex. In ADtex there is cnv.result file which contains the regions of the target regions that have CNVs with the segmentation ratio information. I want to integrate the output of both ADtex and FREEC. So I need figure out a way to narrow down the CNVs of ADtex to list of potentially significant ones and then compare the regions of CNVs from both the tool. The order of CNVs by FREEC after significance assesment is around 110. However for the ADtex output I have regions over 6k which have copy gains of 1 or more (CNV 3 or 4). I cannot take all of them to overlap. So I want to narrow down this list and then make a try to compare the result between the two tools. Also in order to annotate the CNVs of ADtex I do not think I should consider all the 6k CNVs. It would be nice what others do with the ADtex output to streamline it for significant CNVs. Even if I have to compare the output of both tool at gene level I would have to consider most significant CNVs from ADtex like that of FREEC. Is there a way to do that with the ADtex output to provide a p-value and then I can consider those which are significant below a p-value threshold? I would like to know how I can do that?
Regards
