Question: removing PCR duplicates

[fgvieira]

Dear all,

should PCR duplicates be removed from the BAM file before running SQUID? I see a message saying that SQUID is removing PCR duplicates but it is quite fast, what makes me think that it is only removing reads that are already marked as duplicates. Is it so?

If not, should I remove duplicates from the BAM and chimeric BAM files?

thanks,