Hi Ben,
Just to be clear, MergeBamAlignment was poorly named, since like all
Picard programs, it will handle either SAM or BAM. Input file format is
detected automatically, and output file format is determined by file
extension. So if CleanSam does what you want on SAM files, it should
work equally well on BAM.
-Alec
On 7/31/14, 1:06 PM, Ben Bimber wrote:
Hi Alex,
Yeah, I assumed something like that. I have also frequently run into
annoyances related to BAMs produced elsewhere and picard's
requirements. Would it make sense to have either, 1) a standalone
CleanBam tool or better CleanSam tool that handles BAMs, or 2) some
more explicit arguments to MergeBamAlignment to make it cleanup a
single BAM more explicitly?
-Ben
On Thu, Jul 31, 2014 at 9:56 AM, Alec Wysoker
<[email protected] <mailto:[email protected]>> wrote:
Hi Ben,
You are right that we should document this better. And, no, I
don't mean CleanSam.
Various aligners do all sorts of strange things to the reads; e.g.
not all the reads are written to the output, reads are
hard-clipped, some attributes in the input don't make it to the
output, etc. MergeBamAlignment takes as input 2 BAMs: an unmapped
BAM that presumably satisfies Picard's validation requirements,
and an aligned BAM. It takes only the alignment information from
the aligned BAM, and everything else from the unmapped BAM, and
produces an aligned BAM that satisfies strict Picard validation.
-Alec
On 7/31/14, 12:25 PM, Ben Bimber wrote:
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] <mailto:[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 <tel:31.07.2014%2017>: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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