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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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For paired-WGS, is it necessary step of markduplicates by PICARD? #825

Open a00101 opened 1 year ago

a00101 commented 1 year ago

"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 ?

tjbencomo commented 10 months ago

Hi - not the cnvkit authors but I believe the note is only referring to targeted amplicon sequencing and not WGS data.