Re: [Samtools-help] picard IlluminaBasecallstoFastq

Tue, 19 Aug 2014 15:05:08 -0700

The pass-filter flag changed in casava 1.8 so that might be where some of the confusion comes from. Previous versions used "Y" if the read passed the Chastity filter and "N" if it didn't.

A couple of options come to mind:
1. Add a command line parameter to indicate if the files are casava version 1.8 (or later)
2. Use the quality score encoding to determine if the files are from casava version 1.8 (or later). In casava 1.8 the quality score encoding changed to phred+33 (to match what the rest of the world has been doing for years). Previous versions used phred+64.

Hope this helps!

Lee



Received from Nils Homer on 8/19/14 5:11 PM:
Hey Abaan,

it looks like your interpretation is correct for the Casava 1.8 read name structure, namely that "Y" means that the read has been filtered, "N" otherwise [1].  The current Picard software outputs "Y" if the read has not been filtered, namely it has passed filtered, "N" otherwise.  Given that this software has been in use for a while, we have to consider how we move forward with this issue, though the change in the code should be trivial.  Thanks for reporting this,

N



On Tue, Aug 19, 2014 at 4:32 PM, Abaan, Ogan (NIH/NCI) [E] <[email protected]> wrote:
Any thoughts any one. What does Y and N mean in the case of a read pass
of fail filter?

On 8/19/14, 4:26 PM, Alec Wysoker wrote:
> Hi Ogan,
>
> Could you please send your reply to the whole list so that other
> members of my group see it?
>
> Thanks, Alec
>
>
> On 8/19/14, 4:20 PM, Abaan, Ogan (NIH/NCI) [E] wrote:
>> Thank you Alex for the prompt reply. It may very well be but, here is
>> the follow up. I am running rnaseqc on these files, and it labels
>> majority of the reads failed filter as well. That is what got look
>> into all of this to begin with.
>>
>> Are we really sure that Y is meant pass filter, check this out too
>> http://seqanswers.com/forums/showthread.php?t=19891
>>
>> I have a feeling "N" was meant for passed filter
>>
>> Ogan
>>
>>
>> On 8/19/14, 3:50 PM, Alec Wysoker wrote:
>>> Hi Ogan,
>>>
>>> I believe the wikipedia article is not very clear.  Y means passed
>>> filter.  At least that is what IlluminaBasecallsToFastq intends it
>>> to mean.
>>>
>>> -Alec
>>>
>>> On 8/19/14, 3:41 PM, Abaan, Ogan (NIH/NCI) [E] wrote:
>>>> I have tried the most current version of picard as well, but seem to
>>>> have the same issue. When I run IlluminaBasecallstoFastq, with
>>>> read-format as casava_1_8, I get nice fastq files with proper headers,
>>>> but, almost all of the reads are labelled "Y" for pass-filter
>>>> failed or
>>>> not. I see from the QC metrics that most of the reads passed
>>>> filter, so
>>>> why picard is labeling them as failed filter. I think "Y" stands for
>>>> failed filter and "N" stands for not failed filter, at least thats
>>>> what
>>>> it says here http://en.wikipedia.org/wiki/FASTQ_format "Y if the
>>>> read is
>>>> filtered, N otherwise"
>>>>
>>>> Can anybody help me out to sort the problem?
>>>>
>>>> Thanks
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Samtools-help mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>>
>>
>


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