Re: [Vcftools-help] HELP: How is QUAL score recalculated by vcf-merge?

[Peter J. <tr...@gm...>]

Isn't the QUAL defined as "Phred-scaled probability of all samples being 
homozygous reference"? If that is correct, I think it follows that we 
merge two data sets with QUAL = Q1 and Q2, respectively, the merged QUAL 
will be greater than both Q1 and Q2, since
P(all sample are ref/ref) <= P(all samples in a subset are ref/ref)

Thanks,
Peter



On 10/05/2012 11:30 PM, Mark Aquino wrote:
> Thanks Petr, so you recommend using the geometric mean of the quality scores where available and to omit no calls from the calculation?
>
>
> Best,
> Mark
> Sent from my iPhone
>
> On Oct 5, 2012, at 3:33 AM, "Petr Danecek"<pd...@sa...>  wrote:
>
>> Hi Mark,
>>
>> the current implementation is somewhat naive. It is similar to geometric
>> mean but weighted by the number of samples in the VCF, so that when a
>> VCF with one sample is being merged with a VCF with many samples, the
>> quality from the first does not override the latter. Better would be to
>> use the individual quality scores, but this is not always available.
>>
>> Petr
>>
>> On Thu, 2012-10-04 at 21:03 +0000, Mark Aquino wrote:
>>> When multiple quality scores are combined from different VCF files
>>> (via vcf-merge), how is the NEW quality score in the multi-sample vcf
>>> calculated using the individual quality scores from the single-sample
>>> vcfs? I've tried everything from geometric means to converting back to
>>> p-values and re-calculating the Phred score and nothing gives me the
>>> same value that VCFTools calculates!
>>>
>>>
>>>
>>>
>>> Thanks,
>>> Mark
>>
>>
>>
>> -- 
>> 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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