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Can I use GISTIC2 for CNV data from targeted sequencing?
I have targeted panel sequencing data. The panel size is 1.2 Mbp with 33,524 probes targeting a total of 382 genes, including entire exons of 199 genes.
I got segmented log2 ratios and SEG files using CNVkit from this targeted bam files. I would like to check driver events using GISTIC2.
length-based filtering of arm-level events greatly improves the sensitivity of GISTIC. But my data is targeted, so I worry that the algorithm will work. Can I use CNV data from targeted sequencing instead of whole exome sequencing or whole genome sequencing as an GISTIC2 input?