variant calling in polyN region using HaplotypeCaller

Hi all,

I am using GATK HaplotypeCaller to call the variant, which lies in polyN complex region.

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R /data/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa -D wellwise.vcf -L wellwise.vcf -I region.bam -o test.vcf -bamout region.bamout.bam

It is obvious that the most of the alleles represent T at the position in the attached image, either in original or bamout bam file.

However, the vcf file only shows that there are 16 reads representing C while there are only 7 reads for T, which is largely different against the IGV shots.

##reference=file:///data/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  GWI174_combined
22  42528028    .   C   T   90.73   .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.061;ClippingRankSum=0.000;DP=128;ExcessHet=3.0103;FS=4.365;MLEAC=1;MLEAF=0.500;MQ=59.93;MQRankSum=0.756;QD=3.94;ReadPosRankSum=1.554;SOR=1.785    GT:AD:DP:GQ:PL  0/1:16,7:23:99:128,0,418

Can @Sheila or others help me to fix the issue?

Best,
Junfeng