A Variant which is supported by 21 reads in IGV is not called by HaplotypeCaller...

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

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