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suggest to merge MosaicHunter into GATK

Yyx2626Yyx2626 Peking University, Beijing, ChinaMember
edited April 2018 in Ask the GATK team

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?

Issue · Github
by Sheila

Issue Number
3041
State
closed
Last Updated
Assignee
Array
Closed By
chandrans

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited April 2018

    @Yyx2626
    Hi Adam,

    Let me see if one of the team members can get back to you with more information.

    -Sheila
    EDIT: It seems you have posted here as well. Someone will most likely follow up there.

    Post edited by Sheila on
  • manolismanolis Member ✭✭

    Hi,

    about SNV and Indel discovery, do you have any news about a GATK4 tool/pipeline specific for mosaicism analysis (mosaic vs its normal)? or are you planning something?

    For now I'm using Mutect2, tumor-normal paired.

    All the best

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @manolis The MosaicHunter developers have not followed up with us yet. Using Mutect2 is a reasonable solution, and in fact our proposal for MosaicHunter was to absorb a few of its filters into FilterMutectCalls without changing anything else about Mutect2.

    I believe the Kathiresan lab is also using Mutect2 for mosaicism, in case you wish to compare experiences. If you have any suggestions or requests we would be very interested.

  • manolismanolis Member ✭✭

    Hi @davidben, is perfect for me to use "Mutect2/GATK v4 pipelines" for mosaicism. Many thanks for your information.
    Best!

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