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Variant with great support not called.
This SNP has 30 reads supporting it with most of them being mapq60 and good fred scores.
using version 3.4-46-gbc02625
and my command was
java -jar ~/GenomeAnalysisTK.jar -R /mnt/opt/refdata/fasta/hg19/hg19.fa -I /mnt/park/gemcode/haynes/rfa/RFA_phaser5/_SNPINDEL_PHASER_BAM/ATTACH_SERAFIM/fork0/files/output.bam -T HaplotypeCaller --genotyping_mode DISCOVERY -L chr3:33100000-33300000 -stand_emit_conf 10 -stand_call_conf 30
Let me know if you want more info or want me to submit a detailed bug report with relevant files.