Re: [Samtools-help] incorrect SamFormatException in PicardTools ?

[Alec W. <al...@br...>]

Hi Wolfgang,

I will not argue that Picard's behavior in this regard is absolutely 
conforming to the spec.  If you troll through the list archive I believe 
you will find that this had been discussed before.  We have found this 
level of validation to be very useful.  If these alignments are coming 
from BWA, we recommend using MergeBamAlignment which will create a BAM 
that satisfies Picard's admittedly very strict validation.  Or, you can 
disable the validation.

-Alec

On 7/31/14, 11:40 AM, Wolfgang Maier wrote:
> On 31.07.2014 17:26, Alec Wysoker wrote:
>> See the Picard FAQ:
>>
>> http://sourceforge.net/p/picard/wiki/Main_Page/#q-why-am-i-getting-errors-from-picard-like-mapq-should-be-0-for-unmapped-read-or-cigar-should-have-zero-elements-for-unmapped-read
>>
>> -Alec
>>
> Well, that shows that it is known behavior of PicardTools, but still, is
> it *correct* behavior given the format specifications ?
>
>> On 7/31/14, 4:36 AM, Wolfgang Maier wrote:
>>> Hi,
>>>
>>> I've tried to run SamToFastq on a sam file with unaligned reads. Right
>>> on the first line picardtools complains:
>>>
>>> Exception in thread "main"
>>> htsjdk.samtools.SAMFormatException: Error parsing text SAM
>>> file. MAPQ must be zero if RNAME is not specified; Line 4
>>> Line:
>>> HWI-EA332_1_2_662_117/1	4	*	0	255	*	*	0	0
>>> CCACACTACACCCTAACACACCCTAATCTAACCCTGGCCAACCTGTCTCTC
>>> BBBBCCCCBB@BCB?CBC@ABB?<>AB?CBCBB@BC>BB@BB7BCB<BCA?	RG:Z:007
>>>
>>> After consulting the sam format specifications I think that this
>>> behavior is incorrect.
>>> The read has bit 4 set in the FLAG field and with that "no assumption
>>> can be made about RNAME, POS, CIGAR, MAPQ", so picard shouldn't even
>>> look at MAPQ here.
>>> Even if it did, I don't know whether it should expect MAPQ to be zero in
>>> the absence of RNAME as a MAPQ value of 255 "indicates that the mapping
>>> quality is not available", which seems to be about as reasonable as
>>> setting it to 0.
>>>
>>> Please correct me if I'm getting this wrong,
>>> Wolfgang
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Infragistics Professional
>>> Build stunning WinForms apps today!
>>> Reboot your WinForms applications with our WinForms controls.
>>> Build a bridge from your legacy apps to the future.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Samtools-help mailing list
>>> Sam...@li...
>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>
>> ------------------------------------------------------------------------------
>> Infragistics Professional
>> Build stunning WinForms apps today!
>> Reboot your WinForms applications with our WinForms controls.
>> Build a bridge from your legacy apps to the future.
>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>>
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
> Reboot your WinForms applications with our WinForms controls.
> Build a bridge from your legacy apps to the future.
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> _______________________________________________
> Samtools-help mailing list
> Sam...@li...
> https://lists.sourceforge.net/lists/listinfo/samtools-help