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I am running some initial experiments with Mutect2 and am seeing some seemingly very clear calls being missed. These calls are made by the original Mutect (and other callers). Stepping through the code for one of the calls of interest, it seems that calls are only made if both the tumor LOD and normal LOD exceed thresholds. Should not the normal LOD be allowed to be lower than the threshold?
From SomaticGenotypingEngine (when this passes, the call is created):
if (tumorLod >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLod >= MTAC.INITIAL_NORMAL_LOD_THRESHOLD)
-T MuTect2 -R /home/lmose/reference/chr7/chr7.fa -I:tumor /home/lmose/dev/edico/mutect/egfr1/tumor.bam -I:normal /home/lmose/dev/edico/mutect/egfr1/normal.bam -L /home/lmose/dev/edico/mutect/egfr1/test.bed -o /home/lmose/dev/edico/mutect/egfr1/precompiled/test.vcf --debug