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Running HaplotypeCaller on a multi-lane sample

Hello,

I am interested in running HaplotypeCaller for a multi-lane sample. What is the best way to do this? I followed the protocol here (https://software.broadinstitute.org/gatk/documentation/article?id=6057) which states to run MarkDuplicates and BQSR before HaplotypeCaller, which I did. I fed the new BAM file into HaplotypeCaller but get an error with a corrupt gVCF file. Am I meant to merge the read groups into a single read group before using HaplotypeCaller?
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