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
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Originally posted by jkbonfield View PostThanks 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
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Originally posted by nilshomer View PostCheck out the headers used in the 1000 Genomes Project. They should have all three technologies represented.
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
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Originally posted by jkbonfield View PostThe 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.
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SAM platform values
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.Tags: None
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