I am using GATK v220.127.116.11, and I ran HaplotypeCaller in two libraries of the same sample. Although a given region is similarly variable in both libraries, GATK has only called variants in one of them. This occurs in multiple regions of the genome.
I am attaching an IGV screenshot with an example of this situation.
The command I used was:
gatk HaplotypeCaller -R reference.fasta -I strain.mkd.bam -O strain.vcf -ploidy 2 --genotyping-mode DISCOVERY --standard-min-confidence-threshold-for-calling 30 -bamout strain.GATK.bam
Can you please help me understanding what is going on?
Thanks in advance.
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