Re: [Samtools-devel] Picard: MarkDuplicates, metrics file giving 'Unknown Library'

[Keiran R. <kr...@sa...>]

Hi Tim,

Yep, bug at my end, changed the id source in a branched copy and not  
the main.

Cheers,


Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100
kr...@sa...

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.



On 19 Nov 2009, at 15:54, Tim Fennell wrote:

> Hi Keiran,
>
> I don't think there have been any changes to how MarkDuplicates  
> works in that time - so this is either a bug/change somewhere else  
> in the SAM reading code or a problem with the data.  The only time  
> it should use "Unknown Library" is when either the sam record  
> doesn't have an @RG attribute or the matching @RG in the header does  
> not have an LB attribute.
>
> -t
>
> On Nov 19, 2009, at 10:48 AM, Keiran Raine wrote:
>
>> Hi,
>>
>> Was a change applied in Picard that causes long library names to be  
>> returned as 'Unkonwn Library'?
>>
>> A previous run of the same data (using 1.05/6 I think) returned the  
>> following:
>>
>>             'LB996_test3_1_100cycle_test_unarch_1' => [
>>                                                         4279552,
>>                                                         289830239,
>>                                                          
>> '0.0147657194596593',
>>                                                         285550687
>>                                                       ]
>>
>> The current release 1.07 gives:
>>
>>             'Unknown Library' => [
>>                                    4279552,
>>                                    289830239,
>>                                    '0.0147657194596593',
>>                                    285550687
>>                                  ]
>>
>> The figures are not a direct mapping to the metrics file, but are  
>> consistent.
>>
>> Thanks
>>
>>
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 2100
>> kr...@sa...
>>
>> 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.
>>
>>
>>
>>
>> -- The Wellcome Trust Sanger Institute is operated by Genome  
>> Research Limited, a charity registered in England with number  
>> 1021457 and a compa ny registered in England with number 2742969,  
>> whose registered  office is 2 15 Euston Road, London, NW1 2BE. 
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-- 
 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.