Dear Jonathan,
It was good to meet you last Friday.
I would be happy to use QCTOOL to compile an exclusion list. My
problem is that I can't seem to get it to work on gzipped VCF files.
The error message is the following:
Opening genotype files :
[ ] (0/1,0.0s,0.0/s)
Error (genfile::MalformedInputError): Source "test_chr20.vcf.gz" is
malformed on line 1..
I attach a small VCF file that I could not get to work. I used the
command
qctool -g test_chr20.vcf.gz -snp-stats chr20_snp-stats.txt
Many thanks,
Klaudia
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----------------------------------------------------------
Klaudia Walter, Ph.D.
Statistical Geneticist
Genomics of Quantitative Variation Group
The Morgan Building
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1HH, UK
Tel: +44 (0)1223 834244 (ext. 8688)
Email: [log in to unmask]
-----------------------------------------------------------
On 8 May 2012, at 13:04, Jonathan Marchini wrote:
> Hi Klaudia,
>
> Just a quick follow-up on your question on Friday about SNPTEST. See
> below. Gavin thinks it will be possible but we are probably looking
> at around 3 weeks before this could get released.
>
> Regards,
>
> Jonathan
>
> -------- Original Message --------
> Subject: Re: SNPTEST question
> Date: Tue, 8 May 2012 11:43:36 +0000
> From: Gavin Band <[log in to unmask]>
> To: Jonathan Marchini <[log in to unmask]>
>
>
>
> Hi Jonathan,
>
> Sorry for not getting back to you sooner (in Malawi at the moment.)
>
> I guess the answer is
>
> A) It wouldn't be hard to add this; it depends a bit on which MAF
> you want to filter on - across everyone? or just in controls? etc.
> B) If desperate, they could always use QCTOOL to make an exclusion
> list first.
>
> Thanks,
> gav.
>
> On 4 May 2012, at 12:39, Jonathan Marchini wrote:
>
>> Hi Gavin,
>>
>> How quick would it be to add an option in SNPTEST to only run tests
>> at SNPs within a range on MAF? I'm visiting the Sanger and some
>> people here would find it very useful.
>>
>> J
>>
>> -- o__ Jonathan Marchini
>> c/ /'_ Department of Statistics, University of Oxford
>> (+) \(+) 1 South Parks Road, Oxford, OX1 3TG
>>
>> tel : ++44 1865 271125 web : http://www.stats.ox.ac.uk/~marchini/
>>
>>
>
>
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