For paired-WGS, is it necessary step of markduplicates by PICARD?

[a00101]

"Whole-genome sequencing and targeted amplicon capture" says:

"Do not mark duplicates in the BAM files for samples sequenced by this method"

However, in the BAM file preparation, it is written as follows.

"For best results, use an aligner such as BWA-MEM, with the option to mark secondary mappings of reads, and flag PCR duplicates with a program such as SAMBLASTER, SAMBAMBA, or the MarkDuplicates script in Picard tools, so that CNVkit will skip these reads when calculating read depth."

which one is recommended ?