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Great job through the years, really appreciated your dedication and fast response to questions!
Hi Sheila, I think I figure out the issue, I found http://gatkforums.broadinstitute.org/gatk/discussion/3061/haplotype-score-and-phasing helpful explaining the HC not emit haplotypes, but try to best estimate the genotypes with high confidence. And…
Thanks for your explanation, the bam file was downloaded from 1000 Genomes Project, the famous NA12878 sample, it is a huge bam file from exome sequencing and mapped reads using illumina technology. I have used the following command to call the vari…