Just as a general rule, if we have a very interesting variant, we have many metrics to judge the variant, from mapping quality to strand bias to coverage ,..etc. If the variant passes most filters on such metrics and fails one, so simply discard just because it fails one? I feel okay to discard if the variant has low mapping quality, even if high coverage and no strand bias, .etc.
But for other metrics, if it fails any, just discard? Could we lose interesting variants then? What do you do?