Comments (6)
I think this is a good idea. For the longest time we've all been writing PL:illumina for the various Illumina instruments. It's likely that at least with the new chemistry on the NextSeq that we'll want to be able to identify NextSeq 2-color chemistry data vs. SBS 4-color. And with so many tools relying on PL I'm hesitant to change the value there.
-t
On Jan 29, 2014, at 3:46 AM, Keiran Raine [email protected] wrote:
Hi,
As PL is a restricted list could PM, 'Platform Model', be added to the RG header definition? This would be an unrestricted text field allowing for more detailed information about the machine generating the data.
Regards,
Keiranโ
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Any chance this will happen? I notice that there has been a new spec version since this request was created.
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Since this tag was suggested, there's been an optional alignment aux tag added and a small error corrected. So there hasn't really been a whole new spec version released; it's just that now that the infrastructure is in order, it's very easy to regenerate the PDFs on the website so we do so after each little commit.
Would you like to propose some text describing PM, suitable for the table in ยง1.3?
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Thanks for the clarification. How about (inserted between PL and PU):
Platform Model: more detailed description of platform, e.g. 'HiSeq 2500'. Field is not controlled, however appropriate PL should be specified when using this tag.
from hts-specs.
Wouldn't that be "Platform Model" not Unit?
-t
On Apr 2, 2014, at 5:59 AM, Keiran Raine [email protected] wrote:
Thanks for the clarification. How about (inserted between PL and PU):
Platform Unit: more detailed description of platform, e.g. 'HiSeq 2500'. Field is not controlled, however appropriate PL should be specified when using this tag.
โ
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from hts-specs.
Sorry yes, correcting now
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Related Issues (20)
- VCF: The "PASS" filter should be explicitly listed as optional.
- Missing VCF 4.4 test/validation files
- vcf: Valid contig ID in failed example HOT 1
- vcf: Define Number value P
- Best encoding for use case HOT 6
- vcf: Clarify statuses of DPADJ, CNADJ, and CICNADJ INFO keys
- Issue with 16 bit `N CIGAR OP` field with Long Reads HOT 3
- Clarify padding base for symbolic alleles HOT 4
- Storing definitions for custom tags used in SAM file HOT 1
- vcf: Contig name rules contradiction HOT 1
- vcf: Constrain CHROM record field with the same contig header record ID rules HOT 1
- bam: Explain the use-case of the reference information section HOT 2
- sam: Quality score ambiguity when sequence is a single base HOT 2
- vcf: Failed filter names should disallow "PASS" and MISSING HOT 1
- vcf: Failed example has irrelevant error
- sam: Add PL value "MGIG400" as seen in the wild HOT 5
- sam: Clarify the usage of UTF-8 characters in header HOT 3
- sam: Define format of read group predicted median insert size HOT 2
- sam: Irrelevant test failure in `aux.fail-f1.sam` HOT 1
- sam: Consider more conventional format versioning HOT 6
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