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Consensus genotype of MUTECT1, MUTECT2, Varscan, Muse and Somaticsniper

Hi All,

Suppose I apply multiple methods such as MUTECT1, MUTECT2, Varscan, Muse and Somaticsniper to call mutations for one sample, How to merge them or how to obtain Consensus genotypes for this sample?

In the following Figure, I showed three method to call mutaiton for one sample and saved as VCF files. How to do the consensus for this sample (VCF file)?

Thanks

enter image description here

consensus mutation bcftools
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updated by axel.kunstner • axel.kunstner • written by Shicheng Guo Shicheng Guo

1 answer

Hi,

probably, you already solved this issue. Recently, a method called somaticCombiner was published in Scientific Reports which handles this problem as well:

https://www.nature.com/articles/s41598-020-69772-8

Best, Axel

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written by axel.kunstner • axel.kunstner

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