Needed gatk latest version pipline for variant calling

Question

[Mbillah]

What is the need for RealignerTargetCreator, BaseRecalibrator, MarkDuplicates, IndelRealigner in the latest version of Gatk. Is their any update pipline for variant calling by gatk?

[WouterDeCoster]

What was unclear about the official best practices?

[Mbillah]

So RealignerTargetCreator, IndelRealigner is not necessary in update version? I am confused that, is it enough to find out variants: reads -> align -> Mark Duplicate -> then

gatk HaplotypeCaller -R reference.fasta -I sample1.bam -O variants.vcf

TIA