Entering edit mode
5.6 years ago
Mbillah
▴
140
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?
What was unclear about the official best practices?
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