[ensembl-dev] VCF question

[Laura Stephen]

>From the header of the files I suspect Mark is refering to

##FORMAT=<ID=CB,Number=1,Type=String,Description="Called by S(Sanger),
M(UMich), B(BI)">

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/paper_data_sets/a_map_of_human_variation/low_coverage/snps/

thanks

Laura

On Thu, Sep 22, 2011 at 9:39 AM, Laura Clarke <laura at ebi.ac.uk> wrote:
> From the header of the files I suspect Mark is refering to
>
> ##FORMAT=<ID=CB,Number=1,Type=String,Description="Called by S(Sanger),
> M(UMich), B(BI)">
>
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/paper_data_sets/a_map_of_human_variation/low_coverage/snps/
>
> thanks
>
> Laura
>
>
> On Thu, Sep 22, 2011 at 8:52 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Since you didn't get a reply:
>>
>> I guess you can ask on the VCF tools mailing list:
>> http://sourceforge.net/mail/?group_id=279407
>>
>> Or you could contact the data providers and complain for not
>> documenting their files inline as the format suggests:
>> http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40
>>
>>
>> Cheers,
>> Dan.
>>
>> On 15 September 2011 22:15, Mark Aquino <aquinom85 at me.com> wrote:
>>> Hello,
>>>
>>> I have a general VCF format question that I'm having a bit of trouble answering and was hoping someone could help me.  I apologize if this is not the correct forum for requesting this type of information.  At any rate, in the genotype field there are usually fields GT:DP:FT:GL:GQ:HQ in VCF 4.0, but I'm looking at some 1000 genomes data and there is a CB field with values in the individual genotype data SMB, MB, SM, SB, etc.  Could anyone inform me what the CB signifies and what the SMB letter codes mean?
>>>
>>> Thank you,
>>> Mark Aquino
>>>
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>>
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>