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
>
>
>
>
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