AD in VCF doesn't match BAM
I'm using GATK to call variants in my RNA-Seq data. I'm noticing something strange, perhaps someone can help? For a number of sites the VCF is reporting things I cannot replicate from BAMs. How can I recover the reads that contribute to a variant call? Here is an example for 1 site in 1 sample, but I've observed this at many sites/samples:
$ grep 235068463 file.vcf chr1 235068463 . T C 1795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.530;ClippingRankSum=-0.535;DP=60;FS=7.844;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.401;QD=29.93;ReadPosRankSum=3.557 GT:AD:DP:GQ:PL 0/1:5,55:60:44:1824,0,44
60 reads, 5 T, 55 C.
But loading the bam in IGV, I do not see any T reads. Similarly:
$ samtools view -uh file.md.realn.bam chr1:235068463-235068463 |samtools mpileup - |grep 235068463 [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 chr1 235068463 N 60 cCCccccCCCcccccCcccccccccCCCccCCCCCcCcccccCCCcCcCCccCCCCccCC >CA@B@>A>BA@BCABACCC:@@ACABBBCAACBBCABCB@CABBAB?>A?CBBAAAABA
There are just 60 C's at that location. How do I decide what the genotype here is? C/C or C/T ?
For methodology I'm using gatk/3.2.0. I tried using HC from gatk/3.3.1 and got the same result. The bam and vcf files come from the final two lines:
-2 pass STAR