Test-drive the GATK tools and Best Practices pipelines on Terra
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suggest to merge MosaicHunter into GATK
Hello. I am Adam Yongxin Ye, a PhD candidate in Peking University, supervised by Prof Liping Wei.
We have developed MosaicHunter, a bioinformatic tool that can identify postzygotic single-nucleotide mosaicisms (with allele fraction deviated from homozygous 0, 1 and heterozygous 0.5) in bulk sequencing data of a single sample without matched control. After I had the recent lectures on GATK4 tutorial in Beijing, I thought it might be great to merge MosaicHunter into GATK framework, especially for the local assembly function in HaplotypeCaller and Mutect2, to increase the sensitivity & specificity and even extend for mosaic indels, as well as to make MosaicHunter easy for more users to use.
MosaicHunter utilized GATK preprocessing, distinguished mosaicisms from germline homozygous and heterozygous sites by a Bayesian genotyper, and applied several stringent hard filters. MosaicHunter has been published (https://academic.oup.com/nar/article/45/10/e76/2962179 and http://www.nature.com/articles/cr2014131) and is publicly available (http://mosaichunter.cbi.pku.edu.cn/ and https://github.com/zzhang526/MosaicHunter (with source code in java)).
So I wonder if GATK team is interested in this suggestion. Could someone or may we contribute it into GATK?