Is there a way to call somatic mutations from methylation sequencing data？
I am trying to detect somatic snv from methylation sequencing data. I am taking the intersection of the results from bs-snper and gatk mutect2 process to try to obtain somatic variation. I am not sure whether it is reliable. Do you have any better methods or suggestions? Thanks！
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Do you have matched normals? In general methylation data are considered quite noisy so you might get a lot of spurious calls introduced by the bisulfite treatment rather than actual variants. It's suboptimal at best.
I used a public normal control from GATK, indeed methylation data would generate a lot of noise to detect mutations, so bssnper was designed to detect snps using methylation data, but there is no good way to get somatic mutations out of it. I don't know if there is a way to get somatic mutation by filtering from snp vcf.
In addition, I have taken the intersection of the results of the bs-snper and gatk mutect2 procedures to get the somatic variation, but the results are less than ideal.