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GBS data and duplicates marking
Hi, I just read this in the Best Practices guide:
"Duplicate marking should NOT be applied to amplicon sequencing data or other data types where reads start and stop at the same positions by design."
That's somehow what happens with GBS data since the sequenced fragments are obtained by cutting at the same place across the genome with a restriction enzyme for all the samples, have I been wrong when dedupping my data before the genotyping? Many thanks!