Hi Michael,
Note that some aligners, e.g. BWA, can now produce split alignments if an
alignment cannot be represented by a coordinate + cigar string. In a group of
SAMRecords representing such an alignment, all but one of them should have the
0x800 supplementary flag set. Newer versions of Picard handle this properly.
I.e. for a given {read name, end number} there should be only one SAMRecord
that has neither 0x800 (supplementary) nor 0x100 (secondary) flag set.
-Alec
On Jun 16, 2014, at 1:08 PM, Rusch, Michael <michael.ru...@stjude.org> wrote:
> We downloaded some BAM files for some public data. We would like to extract
> raw reads and remap. We've had trouble doing this so far for this one
> particular data set using Picard, and after some investigating, the root
> cause seems to be that they have some reads that have more than one primary
> alignment. So, for a given read name and mate (1/2), there are in some cases
> multiple SAM records that do not have the non-primary flag set. This seems
> "wrong" to me. Am I missing something?
>
> In any case, right or wrong, we're having trouble working with it.
> SamToFastq throws an exception, as does SortSam (we were going to sort by
> queryname and then use some simple code to filter out the dups before
> converting to FASTQ). Anybody successfully dealt with this before who could
> provide some advice?
>
> FYI: we're using an old version of picard, so we're trying with a newer
> version in case the newer version can handle it. We're also going to try
> samtools sort followed by the filtering code. But, I thought maybe if others
> had dealt with this, they could enlighten me with their wisdom and save us
> some work reinventing the wheel.
>
> Michael
>
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