Picard and GaTK HaplotypeCaller

Question

[Afzal]

Hello to every one, I have a question that can we directly run the gatk HaplotypeCaller tool without using the Picard tool to mark the duplicates??? Are they affect on final results for variant calling analysis?

Thanks in advance

[prasundutta87]

GATK Haplotypecaller does not mark duplicates but utlises reads marked as duplicates and ignores them for calling variants. You need to use Picard Markduplicates in order to mark duplicates before variant calling.

This should be helpful: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-