Hey Eric,
you can set the VALIDATION_STRINGENCY to SILENT or LENIENT to remove or
reduce the number of checks. In some cases, while the read may be allowed
under the SAM specification, the requirement is essential for the execution
of the program.
I would believe that having the first of pair flag set for an unpaired
reads should only be done in exceptional circumstances, and the data not
shared with others in such a form.
Sincerely,
Nils Homer
On Fri, Sep 12, 2014 at 2:22 AM, Eric Roller <[email protected]> wrote:
> Using version 1.119 I get this error:
>
> First of pair flag should not be set for unpaired read
>
>
> Basically, Picard is complaining that 0x40 is set when 0x1 is unset. However,
> from the samtools specification:
>
> "If 0x1 is unset, no assumptions can be made about 0x2, 0x8, 0x20, 0x40 and
> 0x80."
>
>
> Furthermore, the 0x40 description from the spec says
>
> 0x40 the first segment in the template
>
> For an unpaired read it will be both the first and last segment in the
> template. That doesn't mean it is paired so there should be no error here.
>
>
> Am I missing something?
>
>
> Thanks,
>
> --
> Eric Roller
>
>
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