Re: [Samtools-help] Algorithm for Picard MarkDuplicates

[Feiyu Du <fd...@ge...>]

Thanks a lot !

It's very helpful.


Feiyu


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.
>
> Hope that helps,
>
> -t
>
>
> On Apr 20, 2010, at 1:54 PM, Feiyu Du wrote:
>
>> Hi,
>>
>> I am new to MarkDuplicates. Could someone describe how it works or point
>> to a helpful documentation site ? Also would quality trimming (resulting
>> in varied length of pair ends) have an affect on MarkDup outputs ?
>>
>> thanks a lot,
>>
>> Feiyu
>>
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