Thank you for your very clear answer, it was great help.
... I'm ashamed to ask... what is the dash ( "-" )before redirecting the output?
i.e.: flagstat - > myfile.stats. If I don't use the dash, it gives me a broken
pipe error. I did some googling, still not sure of its meaning.
Kind Regards,
Max
________________________________________
From: James Bonfield <j...@sanger.ac.uk>
Sent: Thursday, April 28, 2016 4:34 AM
To: Tagliamonte,Massimiliano S
Cc: samtools-help@lists.sourceforge.net
Subject: Re: [Samtools-help] number of mapped reads with flagstat
On Wed, Apr 27, 2016 at 09:07:36PM +0000, Tagliamonte,Massimiliano S wrote:
> My two questions:
>
> 1) Is this strategy correct?
Yes, but you can pipe the two together instead of using a temporary
file. This is useful if you don't need to store the version with
duplicates removed. Use -u (uncompressed) for this as it's faster.
> 2) if in step 1) I want to get rid of flag 0x100 and 0x400 (duplicates which
> I marked with Picard), how can I combine the two flags?
They are single-bit values so you can simply add (bitwise OR) them together.
E.g.
samtools view -F 0x500 myfile.sorted.bam | samtools flagstat - > myfile.stats
Each -F does an "OR" op anyway so you can do -F 0x100 -F 0x400 if you
prefer.
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust 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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