SAM platform values

[jkbonfield]

The SAM read group header line (RG) has a PL tag defined as "platform/technology used to produce the read". It doesn't list a controlled vocabulary.

Hunting through the GATK source code I see cases where it checks for "ILLUMINA", "solid" and "LS454" - in those uppercase/lowercase manners. Is this as about official as it gets? Is there a more complete list or synonyms anywhere?

Ideally this should become an official controlled vocabulary.

[nilshomer]

The SAM read group header line (RG) has a PL tag defined as "platform/technology used to produce the read". It doesn't list a controlled vocabulary.

Hunting through the GATK source code I see cases where it checks for "ILLUMINA", "solid" and "LS454" - in those uppercase/lowercase manners. Is this as about official as it gets? Is there a more complete list or synonyms anywhere?

Ideally this should become an official controlled vocabulary.

Check out the headers used in the 1000 Genomes Project. They should have all three technologies represented.

[jkbonfield]

Check out the headers used in the 1000 Genomes Project. They should have all three technologies represented.

Thanks for the idea, I'll do that.

However "all three" is already a fail. I can think of (in order of age) capillary/sanger, 454, illumina, solid, not to mention prototypes from new instruments.

Although 1000 Genomes has not used any capillary data, we do have quite a few mixed assemblies here with old Sanger sequencing data augmented with a mix of newer technologies.

James

[nilshomer]

Thanks for the idea, I'll do that.

However "all three" is already a fail. I can think of (in order of age) capillary/sanger, 454, illumina, solid, not to mention prototypes from new instruments.

Although 1000 Genomes has not used any capillary data, we do have quite a few mixed assemblies here with old Sanger sequencing data augmented with a mix of newer technologies.

James

Hey now, I meant all three as in all three you mentioned. Don't spark a flame.

[jkbonfield]

Sorry, I didn't mean it as a flame. :-)

Just for the record I'm using "Sanger" as the tag for the sanger sequencing method, although it's a bit generic as it'd catch ABI capillary, licor, megabace etc. They all share similar properties as far as error models go so I think it's sufficient.

It would be good to get these codified in the SAM spec though.

James