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MuTec without dbSNP
congratulations for the nice MuTec publication!
I want to use MuTec for contrastive SNP calling in species without existing high quality SNP db (only for some chromosomes partially available). Is it possible to run it without it and which parameter (e.g. --dbsnp_normal_lod, ...) must be adjusted? Any recommendations highly appreciated!
Thanks a lot,
P.S.: Is GATK SNP recalibration needed? Of course it would be better but again dbSNP missing.
P.P.S.: Alternatively, I could try to generate a SNP db myself. However the sample number limits the quality of it.