Needed gatk latest version pipline for variant calling

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?

gatk

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written 7.9 years ago by Mbillah 14

What was unclear about the official best practices?

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written 7.9 years ago by WouterDeCoster 4.8K

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

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written 7.9 years ago by Mbillah 14

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