Entering edit mode
3.9 years ago
J.F.Jiang ▴ 900
In order to evaluate the drug response of patient, we want to analyze the CNV status of target region.
The panel was developed and synthetized by IDT.
I am wondering if there is any tool to define the CNV status of the target region, such as MET/EGFR/HER2, beside GATK, FREEC, XHMM, since we find the accuracy problem while calling process.
There are many dozens of copy number calling programs. FREEC and XHMM are actually regarded as among the best. What, exactly, is your input data? - genome sequencing, exome / targeted sequencing, microarray, or PCR?
the input data is target sequencing using IDT Capture probe.
Okay, I have had success using FREEC for Exome-seq, which can be regarded as 'genome-wide' target capture. Did you configure FREEC properly? - there are many parameters. Here is an example config file that I used for an Exome-seq sample (Mus musculus):
I tried both FREEC and CNVKit. Both work well, but sometimes came with some bugs, especially depth calculation of FREEC.