Below command is used for the purpose
java -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fa -I 62352575_S28_realigned.bam -L nexterarapidcapture_exome_target_region.bed --genotyping_mode DISCOVERY -o new.vcf
Can you please provide us with more information about this locus, e.g. an IGV screenshot of the target region? Please show that the -L target region covers the variant region.
These 21 reads, can you confirm they are (i) not flagged duplicate (ii) not flagged secondary and (ii) have mates on other contigs? I ask because GATK has safeguards in place to ensure high quality calls. For example, HaplotypeCaller will filter the following types of reads:
You can read more about each of them from this page. Thanks for your feedback.