Re: [Samtools-help] Algorithm for Picard MarkDuplicates

[Sendu B. <sb...@sa...>]

On 26/04/2010 16:19, Tim Fennell wrote:
> Well, treating paired reads as single-end reads will generally result in
> a significant over-marking of duplicates as single end reads are far
> more likely to appear as duplicates than PE reads.

I see. Thank you for all the information.


Other than inter-chromosomal duplicate marking, does picard's algorithm 
do anything that samtools rmdup does not? So if I'm running on chr bams, 
can I just use samtools instead for the speed increase and lower memory 
benefits?



> On Apr 26, 2010, at 11:14 AM, Sendu Bala wrote:
>
>> On 26/04/2010 16:08, Tim Fennell wrote:
>>> Hey Sendu,
>>>
>>> I'm not really sure I understand the question. The way Mark Duplicates
>>> works it actually needs to see each read in a pair to determine
>>> duplicate status, because it needs access to the CIGAR for both reads.
>>> The way this is implemented it doesn't process the read pair until it's
>>> seen both ends - and it knows a read is paired or not based on the
>>> flags.
>>
>> When it doesn't find the other read in the pair, can't it just treat
>> the read as unpaired and do what it would normally do for single-ended
>> duplicate marking? Or could the missing CIGAR information result in
>> some cases where a read is marked as a duplicate incorrectly?
>>
>>
>>> On Apr 26, 2010, at 10:31 AM, Sendu Bala wrote:
>>>
>>>> On 26/04/2010 14:24, Tim Fennell wrote:
>>>>> It will not work optimally - it will only detect duplicates for pairs
>>>>> where it has access to both ends. So if you split your files by
>>>>> chromosome then you'll essentially lose inter-chromosomal duplicate
>>>>> marking.
>>>>
>>>> So even if there's a whole bunch of forward reads stacked up on one
>>>> chr,
>>>> they'll be ignored if their reverse reads aren't in the bam file?
>>>>
>>>> Is that something that can't be changed because these somehow might not
>>>> be 'real' duplicates without knowing the pair information (why
>>>> not?), or
>>>> is it on the to-do list?
>>>>
>>>>
>>>>> On Apr 26, 2010, at 5:35 AM, Sendu Bala wrote:
>>>>>
>>>>>> On 21/04/2010 17:45, Tim Fennell wrote:
>>>>>>> Hi Feiyu,
>>>>>>>
>>>>>>> The algorithm probably does need describing somewhere in detail,
>>>>>>> but I don't believe I have anything handy. Essentially what it
>>>>>>> does (for pairs; single-end data is also handled) is to find the
>>>>>>> 5' coordinates and mapping orientations of each read pair. When
>>>>>>> doing this it takes into account all clipping that has taking
>>>>>>> place as well as any gaps or jumps in the alignment. You can
>>>>>>> thus think of it as determining "if all the bases from the read
>>>>>>> were aligned, where would the 5' most base have been aligned".
>>>>>>> It then matches all read pairs that have identical 5' coordinates
>>>>>>> and orientations and marks as duplicates all but the "best" pair.
>>>>>>> "Best" is defined as the read pair having the highest sum of base
>>>>>>> qualities as bases with Q>= 15.
>>>>>>
>>>>>> Am I right in thinking it will work correctly on a bam that has
>>>>>> been split by chromosome? Or will something not work quite right if
>>>>>> one read of a pair is missing because it mapped to a different
>>>>>> chromosome?
>>>>>>
>>>>>>
>>>>>> -- 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
>>>> 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
>> 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 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.