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I'm analyzing a tumor sample and a healthy sample from the same patient. I want to use sciClone to look at tumor clonality. One input is the genomic regions that need to be excluded due to LOH. I have both WES and WGS.
Is there currently a "gold standard" for which tool will return the most robust regions?
The sciClone paper mentions VarScan2, APOLLOH, HMMScan? Are these still state of the art?
Is it feasible to calculate LOH programmatically without the need of external software?
Answer from @fabio-marroni, converted from comment:
WARNING! Self-promotion! We published a freely-available tool for detection of LOH (and also redeuction fo homozygosity). Here you find the link to the paper and therein will find the link to the software. We compared with other tools that you might also try to see which one is the best performing. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466433/
