Hi Keiran, The -c option clears the duplicate flag and removes any 'dt' or 'do' tags on a read prior to duplicate marking. I added it by request so that a mix of duplicate marking programs did not give inconsistent results.
There is no performance advantage, markdup does not take into account any previous information. Is this what you wanted to know? Andrew On 2020-06-12 13:29, Keiran Raine wrote: > Hi, > > Can someone clarify the behaviour of "Clear previous duplicate settings and > tags" please? > > If data has been duplicate marked at the "lane" level and then merged and > passed into markdup again, should this be in use? Does it give performance > advantage by reusing previous information? > > Thanks, > > Keiran Raine, M.Sc., MBCS > > Principal Software Developer > > Cancer, Ageing and Somatic Mutation > > Wellcome Sanger Institute > > k...@sanger.ac.uk > > Office: D3-19 > > Ext: 4983 > > Please note that due to childcare requirements during the Covid lockdown I am > generally not available after 4pm. -- The Wellcome Sanger Institute is > operated by Genome Research Limited, a charity registered in England with > number 1021457 and a company registered in England with number 2742969, whose > registered office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_samtools-2Dhelp&d=DwICAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=iKRz7N6xL3uJ6tuuPlViiQ&m=M1uS2vu4yCY2n1GopIIHRS3btcMUzjwvBQAfID-qilM&s=RhOZbZVZJCVybTLaD7RHPvlJxrjvqKiIMemJ_C0gDns&e= -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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