SNAP seems to put some @RG-* tags into the alignment section
This shouldn't happen for SM and PL tags as they are either not defined or have different meanings.
According to the SAMFile Spec
@RG-SM is the Sample name
SNAP will put this into the alignment section as
SM:Z:SomeSampleName
However SM is defined in the SAMFile spec as "SM i Template-independent mapping quality"
which has type "i" (Singed 32-bit integer).
Tools such as qProfiler trying to convert the string into integer will fail.
Another tag is @RG-PL
Which appears as
PL:Z:SomePlatform
But this is actually not a defined TAG in the spec
SNAP seems to put some @RG-* tags into the alignment section This shouldn't happen for SM and PL tags as they are either not defined or have different meanings.
According to the SAMFile Spec @RG-SM is the Sample name SNAP will put this into the alignment section as SM:Z:SomeSampleName However SM is defined in the SAMFile spec as "SM i Template-independent mapping quality" which has type "i" (Singed 32-bit integer). Tools such as qProfiler trying to convert the string into integer will fail.
Another tag is @RG-PL Which appears as PL:Z:SomePlatform But this is actually not a defined TAG in the spec
An Example record that fails in qProfiler