在看gatk4的mutect2結(jié)果時(shí)發(fā)現(xiàn)，其的AF并非是AD相加除以的結(jié)果。
One possibility is that there are reads supporting one or the other
allele that aren't being counted in the AD values because they're not
considered informative for the purposes of the genotyping, but they are
being counted in the allele fraction estimation. Another is that there
are reads supporting some other allele that is not called, but is
present in some minor fraction, and is therefore counted in the AF
estimation as well. In both cases you would see them if you look at the
read data in the bam file (preferably the "bamout" that can be generated
as documented for HaplotypeCaller).
https://software.broadinstitute.org/gatk/documentation/article.php?id=6005
有描述：Because the DP in the INFO field is unfiltered and the DP in the FORMAT
field is filtered, you know none of the reads were filtered out by the
engine's built-in read filters.
mutect2的一些文檔：
https://gatkforums.broadinstitute.org/gatk/discussion/11136
https://gatkforums.broadinstitute.org/firecloud/discussion/comment/45055
