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min base quality and min mapping quality and -rf flag
I wan to apply two filters for the haplotype caller in the GVCF mode. These are min base quality and min mapping quality.
-mbq 20 -mmq 30
But I am not sure about to specify the read filter flag like this
If I am going to use two filters I must to use two times the rf flag?
-rf MappingQuality -rf BaseQuality
Or how this works? I get the same results without using the rf flag?
Thank you Very much