There is a slowly growing documentation on the new website, please check
the variant calling workflow
http://www.htslib.org/workflow/
You need to use `bcftools call`, not `bcftools view`.
petr
On Tue, 2014-09-23 at 09:25 -0400, jbr950 wrote:
> Good catch - I was trying to use an old version of bcftools with the
> new version of samtools..
>
>
> So I changed that to point to the new version of bcftools, and now:
>
>
> samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup -BQ0
> -d10000000 -l $variantBed -uf ${ref} $bamFile > test.bcf
>
>
>
> So far so good..
>
>
> And then:
> cat test.bcf | samtools-bcftools-htslib-1.0_x64-linux/bin/bcftools
> view -cg -
> Error: Could not parse --min-ac g
>
>
>
> On the other hand, calling: .
> cat test.bcf | samtools-bcftools-htslib-1.0_x64-linux/bin/bcftools
> view-
>
>
>
> does create a nice output, so I'm inclined to let it go with the
> defaults. I don't see equivalent arguments for the -c and -g flags and
> I'm not particularly attached to the use of Bayesian inference,
> although it would be good to understand what differences I can expect
> between the old method (using -c) and the new (sans -c)?
>
>
> Thanks for your time and assistance!
>
>
> Jonathan
>
>
>
>
>
> On Tue, Sep 23, 2014 at 2:40 AM, Petr Danecek <[email protected]>
> wrote:
> This does not look like output from samtools 1.0 - it outputs
> VCFv4.2
>
> petr
>
> On Mon, 2014-09-22 at 14:53 -0400, jbr950 wrote:
> > Hi Petr,
> > Thanks for your reply. I grabbed the
> > samtools-bcftools-htslib-1.0_x64-linux binary and tried
> again.
> >
> >
> > When I'd used Samtools 0.1.18, the issue I emailed about was
> that the
> > number of lines in output varied by .bam file, and I didn't
> understand
> > why lines were being ommitted, and why not in a common
> manner.
> >
> >
> > Using version 1.0 and the same command (I checked on the
> older
> > samtools and it is producing output), I get no output at
> all. Mpileup
> > writes a header and then stops. I have copied and pasted
> the output.
> >
> >
> >
> > My .bed is 3 columns: chr start stop
> > with no header.
> >
> >
> > Any advice appreciated, thanks!
> >
> >
> > Jonathan
> >
> >
> >
> >
> >
> >
> > [mpileup] 1 samples in 1 input files
> > (mpileup) Max depth is above 1M. Potential memory hog!
> > [bcf_sync] incorrect number of fields (0 != 5) at 0:0
> > [afs] 0:0.000
> > ##fileformat=VCFv4.1
> > ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read
> depth">
> > ##INFO=<ID=DP4,Number=4,Type=Integer,Description="#
> high-quality
> > ref-forward bases, ref-reverse, alt-forward and alt-reverse
> bases">
> >
> ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square
> > mapping quality of covering reads">
> > ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred
> probability of
> > all samples being the same">
> >
> ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood
> > estimate of the first ALT allele frequency (assuming HWE)">
> >
> ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood
> > estimate of the first ALT allele count (no HWE assumption)">
> > ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate
> of genotype
> > frequencies">
> > ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based
> HWE test
> > P-value based on G3">
> > ##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio
> of
> > genotype likelihoods with and without the constraint">
> > ##INFO=<ID=UGT,Number=1,Type=String,Description="The most
> probable
> > unconstrained genotype configuration in the trio">
> > ##INFO=<ID=CGT,Number=1,Type=String,Description="The most
> probable
> > constrained genotype configuration in the trio">
> > ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for
> strand
> > bias, baseQ bias, mapQ bias and tail distance bias">
> > ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates
> that the
> > variant is an INDEL.">
> > ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred
> probability of
> > the nonRef allele frequency in group1 samples being larger
> (,smaller)
> > than in group2.">
> > ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior
> weighted
> > chi^2 P-value for testing the association between group1 and
> group2
> > samples.">
> > ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred
> scaled
> > PCHI2.">
> > ##INFO=<ID=PR,Number=1,Type=Integer,Description="#
> permutations
> > yielding a smaller PCHI2.">
> > ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant
> Distance
> > Bias">
> > ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
> > ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype
> Quality">
> > ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods
> for
> > RR,RA,AA genotypes (R=ref,A=alt)">
> > ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="#
> high-quality
> > bases">
> >
> ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand
> > bias P-value">
> > ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of
> > Phred-scaled genotype likelihoods">
> > #CHROM POS ID REF ALT QUAL FILTER INFO
> FORMAT
> >
> >
> >
> > On Thu, Sep 4, 2014 at 5:20 AM, Petr Danecek
> <[email protected]> wrote:
> > Hi Jonathan,
> >
> > these are good questions. Could you please try with
> the latest
> > release,
> > I am happy to answer any remaining issues not solved
> by the
> > upgrade.
> >
> > Cheers,
> > Petr
> >
> > On Sun, 2014-08-17 at 01:34 -0400, Jo R wrote:
> > > Hello,
> > > I'm attemping to get nucleotide frequency
> information at
> > a number
> > > of positions across a number of samples, and am
> having
> > difficulty
> > > interpreting some output. Any insights would be
> > appreciated.
> > >
> > >
> > > I'm running the following command:
> > >
> > >
> > > samtools mpileup -BQ0 -d10000000 -l
> VariantBed.bed -uf
> > $refFile $bam
> > > | bcftools view -bcg - | bcftools view - >
> > > ${sampleName}_validation.vcf
> > >
> > >
> > >
> > > I notice that this command creates an output file
> with
> > > an unpredictable number of rows. Running the
> command using
> > the same
> > > bed file on a set of different .bam files creates
> a set of
> > output vcf
> > > files with a wide distribution in numbers of rows.
> > >
> > >
> > > I presumed that the difference in row numbers
> means that
> > some
> > > positions drop out on some .bam files because
> those samples
> > lacked
> > > coverage where other samples had coverage.
> > >
> > >
> > > If that's the case, though, I don't know what to
> make of
> > lines like
> > > the following one:
> > >
> > >
> > > 1 2160881 . G . 28.2 .
> > > DP=0;VDB=0.0003;;AC1=2;FQ=-30 PL 0
> > >
> > >
> > >
> > > here, it looks like DP=0, but this position still
> got
> > reported in the
> > > vcf output. I also don't see AC1 in the legend
> for INFO
> > tags in the
> > > samtools specification page, so I don't know what
> to make of
> > a value
> > > of 2.
> > >
> > >
> > > So, I am confused. Positions with a positive
> value of DP
> > and DP4 make
> > > sense to me. But why are some positions
> completely ommitted
> > from the
> > > vcf output, and other positions reporting a DP=0?
> > >
> > >
> > > Thanks for any advice.
> > >
> > >
> > > Best regards,
> > > Jonathan
> > >
> > >
> > >
> > >
> >
> > >
> >
>
> ------------------------------------------------------------------------------
> > > _______________________________________________
> > > Samtools-help mailing list
> > > [email protected]
> > >
> https://lists.sourceforge.net/lists/listinfo/samtools-help
> >
> >
> >
> >
> > --
> > 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.
> >
> >
>
>
>
>
> --
> 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.
>
>
>
--
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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