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min base quality and min mapping quality and -rf flag

shinkenshinken IrapuatoMember


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

           -rf MappingQuality

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

Best Answer


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