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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