Hi Andrew,
Great, yes thank you, I can safely ignore this for my workflow.
Thanks again,
Keiran Raine, M.Sc., MBCS
Principal Software Developer
Cancer, Ageing and Somatic Mutation
Wellcome Sanger Institute
k...@sanger.ac.uk<mailto: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.
From: aw7 <a...@sanger.ac.uk>
Date: Friday, 12 June 2020 at 14:40
To: Keiran Raine <k...@sanger.ac.uk>
Cc: "samtools-help@lists.sourceforge.net" <samtools-help@lists.sourceforge.net>
Subject: Re: [Samtools-help] markdup "-c" option [EXT]
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<mailto: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.
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