Dear forum members,

I'm planning to run HaplotypeCaller (using this documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360035890411-Calling-variants-on-cohorts-of-samples-using-the-HaplotypeCaller-in-GVCF-mode ) on several CRAM files (same sample, sequenced at four Sequencing Centers), the idea is to increase coverage and sensitivity in variant calling. I' wondering if there are specific requirements for CRAM files in this setup:

1. Do the RG ID have to be different in each center's CRAM
2. Do RG SM have to be the same in all center's CRAM

Are there any other CRAM format related things to consider ?

Best,

abarysenka