Hi Adrien,
the new, soon to be released, version of samtools can output DP4 for each
sample with "-t dp4". Currently it's available from github as described here
http://samtools.github.io/bcftools/
Petr
On 10 Jul 2014, at 10:40, Rieux, Adrien wrote:
> Hi there,
>
> I’m struggling to request a kind of simple information from samtools.
> I am using samtools on several bam files at the same time. I would like to
> get, for each site of each sample, the number of reads carrying each of the
> different alleles.
> In my vcf file, I have the VP4 field (Number of forward and reverse ref and
> alternative alleles used in variant calling reverse respectively) in the INFO
> fixed field but this corresponds to the counts summed on all individuals. I
> would like to get the same information but for each sample independently. Is
> there a way to do that (besides running mpileup on each sample independently?)
>
> Cheers,
>
> Adrien
>
> I am using the following 2 commands:
> c=/cluster/project9/ All/*.bam
> mpileup -uID -d 1000 -Q20 -f ref.fasta $c | bcftools view -bvcg ->
> snps.raw.bcf &&
> bcftools view snps.raw.bcf | bcftools/vcfutils.pl varFilter -d10 >
> snps.flt_d10.vcf
>
>
> ------------------------------------------------------------------------------------------
> Adrien RIEUX
> Research Associate
> UCL Genetics Institute
> Faculty of Life Sciences
> Department of Genetics, Evolution & Environment
> Darwin building
> LONDON WC1E 6BT
>
> [email protected]
> http://adrienrieux.wordpress.com/
>
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