I am replying to the list so others can benefit from our discussion.
The latest Picard release to support updated Illumina read names is 1.120
while your install is 1.99. You will need to update to this version or the
latest version to get the benefit of this update.
Nils
On Thu, Oct 9, 2014 at 4:08 PM, Nils Homer <nho...@broadinstitute.org>
wrote:
> Could you tell us what version of Picard you are using? There was an
> issue earlier with parsing read names from newer Illumina analysis software.
>
> Nils
>
> On Thu, Oct 9, 2014 at 3:00 PM, Salzberg, Anna <asalzb...@hmc.psu.edu>
> wrote:
>
>> Hello,
>>
>>
>>
>> I am convinced that the optical duplicates count of the Picard
>> MarkDuplicates command is incorrect. When I wrote a script to detect
>> optical duplicates in my dataset, I got only ~1k optical duplicates as
>> opposed to MarkDuplicates ~3 million. I think the problem with
>> MarkDuplicates is tile related because I then wrote a super simple script
>> that simply counts how many duplicates share the same tile, and that was <
>> 4k, that is, 3 orders of magnitudes less than MarkDuplicates! The overall
>> number of duplicates (opticals or otherwise) matched (~7 million). I'm
>> convinced my script is right, as it's so simple.
>>
>>
>>
>> Remove optical duplicates script:
>>
>> https://gist.github.com/annasa/eef7c30152ac296bb49b
>>
>>
>>
>> Count duplicates in same tile:
>>
>> https://gist.github.com/annasa/f5633eecf012153a3ff2
>>
>> Both scripts take as input a sam file sorted on chr and startPos. They
>> also assume that when the sequence name is parsed by ":" then the tile is
>> the 5th field, x the 6th and y the 7th (e.g.
>> HWI-ST1318:119:H89A3ADXX:1:2209:1705:6933, where tile is '2209', x is
>> '1705' and y is'6933'). Finally, they assume that the file is for a single
>> lane, as I was working with such files.
>>
>> This is VERY important for my lab. Please advise as soon as you can.
>>
>> Thank you,
>>
>> Anna
>>
>>
>>
>>
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