Re: [Samtools-help] .sam files from BWA

[Joseph F. <jos...@gm...>]

There's also the issue of sorting, right?

>From memory, I'm thinking the command should be more like:

samtools view -uhS myproject.sam | samtools sort - myproject

... which would give you a by-coordinate sorted bam file: myproject.bam.
The '-u' will make it go faster, since sort can read uncompressed bam. I'm
also suspicious of the -q 100 option ... are you seeing MQ's higher than
that?

HTH,
~Joe




On Wed, May 30, 2012 at 4:51 AM, Tom Blackwell <tb...@um...> wrote:

> Marie  -
>
> One probably needs to provide the '-t' option to samtools view.
> See the samtools unix man page (`man samtools`).  I think that
> bwa does not automatically provide the header information needed
> to convert to .bam.
>
>                                                -  tom blackwell  -
>
> On Wed, 30 May 2012, Philippe Bardou wrote:
>
> > Hi Marie,
> >
> > I don't know how many reads you have in your fastq but perhaps problem
> > come from -q 100 of the samtools view command.
> > Try this for build quality histogram of your mapped reads :
> > cut -f5 myproject.sam | sort -n | uniq -c
> >
> > Regards
> >
> > Philippe
> >> Hi everyone,
> >>
> >> I am using BWA to align paired end reads to a reference genome:
> >>
> >> bwa aln -t 8 myRef myreads1.fq > myalignedreads1.sai
> >>
> >> bwa aln -t 8 myRef myreads2.fq > myalignedreads2.sai
> >>
> >> bwa sampe myRef myalignedreads1.sai myalignedreads2.sai myreads1.fq
> >> myreads2.fq > myproject.sam
> >>
> >> Then I want to create a consensus using mpileup, so I try to convert
> >> my .sam file into a .bam file:
> >>
> >> samtools view -bS -q 100 myproject.sam > myproject.bam
> >>
> >> The .bam file obtained is around 100 octets and I can't use it for
> >> further analyses.
> >>
> >> Can someone tell me where is the problem?
> >>
> >> Thanks in adance!
> >>
> >> All the best,
> >>
> >> Marie
> >
> > --
> >  =======================================================
> >                  --  Philippe BARDOU  --
> >  INRA LGC CS 52627 - 31326 Castanet-Tolosan cedex FRANCE
> >  Tel: +33 (0)5.61.28.57.09  -  Fax: +33 (0)5.61.28.53.08
> >  http://www.sigenae.org/
> >
> >
> >
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-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
joseph.fass -at- gmail.com
530.752.2698 (w)