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Benchmark SNV calls between MuTect2 (GATK 3.7) and CaVEMan ?
I am trying to perform a benchmark between MuTect2 and CaVEMan. I invite anyone who has performed the comparison between them to share the overlap of their results for the calls. My results have shown an overlap of 20%. I also invite the admins to shed some light and share their thoughts with me on this issue (urgent to me).
I have followed the best practices steps and aligned using BWA-mem, cleaned with Picard and did a BQSR on the BAM files. The same BAM files have been used for MuTect2 and CaVEMan. I used public data from TCGA as well as my own data ( 22 samples in total ) where they share approximately 20% (+/- 1%, rarely more) of overlap.
To calculate these overlap, I used the vcf-tools (vcf-compare and vcf-isec).
Also, if you have any references to papers where they have performed a benchmark or at least if they used the two tools, could you please share it ?
Thanks a lot !