Re: [Samtools-help] Algorithm for Picard MarkDuplicates

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

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?


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