Hi Max,
>From the samtools online man pages:
Samtools is designed to work on a stream. It regards an input file `-' as
the standard input (stdin) and an output file `-' as the standard output
(stdout). Several commands can thus be combined with Unix pipes. Samtools
always output warning and error messages to the standard error output
(stderr).
Andrew
On Thu, Apr 28, 2016 at 10:04 AM Tagliamonte,Massimiliano S <
[email protected]> wrote:
> 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 <[email protected]>
> Sent: Thursday, April 28, 2016 4:34 AM
> To: Tagliamonte,Massimiliano S
> Cc: [email protected]
> 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 ([email protected]) | 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.
>
>
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