HaplotypeCaller: --min_base_quality_score vs -stand_call_conf and -stand_emit_conf flags
HaplotypeCaller has a --min_base_quality_score flag to specify the minimum "base quality required to consider a base for calling". It also has the -stand_call_conf and -stand_emit_conf that both of which use a "minimum phred-scaled confidence threshold".
What is the difference between the base quality flag and the phred-scaled confidence thresholds flags in deciding whether or not to call a variant?
Also, why are there separate flags for calling variants and emitting variants? To my way of thinking, calling and emitting variants are one-and-the-same.
Is there any way to specify a minimum minor-allele-frequency for calling variants in Haplotyper? Under the default settings, the program expects 1:1 ratio of each allele in a single diploid organism. However, stochastic variance in which RNA fragments are sequenced and retained could lead to departures from this ratio.
Finally, is there any way to specify the minimum level of coverage for a given variant for it to be considered for calling/genotyping?