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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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Call CNV on RAD data #81

Open X-Mialhe opened 3 years ago

X-Mialhe commented 3 years ago

Hi,

I search to call CNV with RAD human data. Can Control-FREEC helps me ? For now I just try to understand how to configure the soft and do some tests. Do I need to configure like Exome data with window = 0 for exemple ? Or the results will be wrong ?

I have tested to run Control-FREEC with the config file link below and it's run without error but I am not sure about the relevance of the results. I used a BED file containing all the SBFI sites and artificially adding a few hundred BP on each side to "simulate" an analysis window. Do you think this is suitable for this tool or is it a dead end?

Regards, Xavier config_crtl.txt

valeu commented 3 years ago

Hi Xavier, have you finally tried it? I guess you are right to set window=0. But I actually do not know whether you could get nice profiles or not. Alternatively you can also look at OncoCNV, developed for amplicon-sequencing data.