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Mutect1 -> depth of 'PASS' variants
I have used Mutect1 (tumor-control) for calling variants. As mentioned here:
http://archive.broadinstitute.org/cancer/cga/mutect ; that "We currently use cutoffs of at least 14 reads in the tumor and at least 8 in the normal (these cutoffs are applied after removing noisy reads in the preprocessing step)". This means that the variants I get as a result of the analysis should have a depth of at least > 14 in tumor and > 8 in control. However, I do see variants in my resulting vcf file that have DP less than the above mentioned thresholds. I would like to know the explanation for these. Does mutect still calls them 'PASS' based on LOD; or something else should be taken care off here?