mutect2的AF（AF calculation in Mut

在看gatk4的mutect2结果时发现，其的AF并非是AD相加除以的结果。

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的一些文档：

https://gatkforums.broadinstitute.org/gatk/discussion/11136

https://gatkforums.broadinstitute.org/firecloud/discussion/comment/45055