GenotypeGVCFs with same RG tags
Dear GATK forum,
Could you please clarify GenotypeGVCFs behaviour when some gvcfs share the same RG tag?
- in scenario 1 (vertical): we have split single sample into 5 chromosomes using HaplotypeCaller -L option. Would GenotypeGVCFs merge 5 gvcf's correctly or should I merge them beforehand?
- in scenario 2 (horizontal): we have same biological individual sequenced twice in two different runs. The two bam files were HaplotypeCalled separately and then GenotypeGVCFs'd together. Are the results inferior to HaplotypeCalling them together and then GenotypeGVCFs'ing (as suggested in thread below)?
- if so, is the tool that @Geraldine_VdAuwera for recalculating made public in recent GATK versions?
Many many thanks!