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Use mutect2 or UnifiedGenotyper?

ZoeyZoey Member
Hi,

I am currently working on finding the somatic mutations in the tumor (using the sing cell sequencing result). And my final goal is to use these somatic mutations from different regions to build phylogenetic tree for one tumor.

In most papers, they use UnifiedGenotyper to call mutations. Then they acquired the somatic mutations by removing the SNV sites called from the normal sample. As the result is a joint calling result, each sample has all information on all sites, which means it can be easily used to build the phylogenetic tree.

As Mutech2 is designed to call somatic mutations, it may have better ability to do somatic calling. If I merge the Mutech2 result together and check whether the empty value is due to having no variant or having a gap, I can also acquire the vcf results, in which each sample have all information in all sites.

My question is that can Mutech2 result be used in this way? What is the difference between the somatic mutations selected from the snvs called by UnifiedGenotyper and the somatic mutations called by Mutech2?

Thanks for any help.

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Zoey

    First off the UnifiedGenotyper is from GATK3 and we do not support GATK3 tools anymore.

    If I merge the Mutech2 result together and check whether the empty value is due to having no variant or having a gap, I can also acquire the vcf results, in which each sample have all information in all sites.

    Currently Mutect2 result be used in this way because mutect2 does not run in the gvcf mode.

    What is the difference between the somatic mutations selected from the snvs called by UnifiedGenotyper and the somatic mutations called by Mutech2?

    Thats a big question. In short Mutect2 is a graph based variant caller whereas UnifiedGenotyper is a pileup based variant caller. For more details take a look at this doc: https://software.broadinstitute.org/gatk/documentation/article?id=11076

    Also take a look at this doc: https://software.broadinstitute.org/gatk/documentation/article?id=11127

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    In most papers, they use UnifiedGenotyper to call mutations. . .As the result is a joint calling result, each sample has all information on all sites. . . If I merge the Mutech2 result together and check whether the empty value is due to having no variant or having a gap, I can also acquire the vcf results, in which each sample have all information in all sites.

    @Zoey as of the 4.1 release Mutect2 supports joint calling of multiple samples from the same tumor. You just need to specify -I tumor___.bam multiple times in your command. The resulting vcf can then be passes to FilterMutectCalls as usual.

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