Hi Alex,
Using MergeBamAlignment as a cleanup tool (what you seem to be suggesting)
is not something I would have guessed or seen in the docs. Did you mean
CleanSam or is merge doing something extra beyond CleanSam? Is it a
workaround to let you work in BAM versus SAM?
-Ben
On Thu, Jul 31, 2014 at 9:15 AM, Alec Wysoker <[email protected]>
wrote:
> 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
> >>>
> >>>
> >>>
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