Marking heterozygous while there's no reads with ref allele
My first MuTect2 run comes up with something strange: when the read depth is low (I mean in the single digits), the tumor sample would be assigned heterozygous (GT of "0/1") despite all reads have the ALT allele. An example VCF line is as follows:
chr1 1306420 . A G . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=2.41;TLOD=30.99 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:0,9:1.00:9:0:0.00:0,267:0:0 0/0:8,0:0.00:0:0:.:212,0:8:0
While I understand MuTect in general handles heterozygozity more loosely than HaplotypeCaller out of necessity, I'm not expecting a AF=1 would still get a GT=0/1.
For background, MuTect2 as packaged on GATK3.5-release is ran on RHEL6.5. JDK 1.7.0r79 used with -nct 8, bundled dbSNP, and current COSMIC file I indexed myself.