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Error running haplotypecaller (v3.3)
I am running the haplotypecaller on multiple samples all but one work correctly with the following commands, however one is resulting in a binary file instead of the gvcf. Any suggestions how to fix this?
HaplotypeCaller -i map/30.rmdup.bam -o gvcf/30.gvcf -r reference_F.fasta -p 10 -a gvcf/30.gvcf -g -e hc.log