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Can BQSR work on data coming from BGISEQ-500 and how to set the Read Group PL ?

Hi GATK team,
I have two questions when using GATK4:
1) Can Base Quality Score Recalibration (BQSR) work on data coming from BGISEQ-500? Please see this paper for more information about this sequencing platform: www.ncbi.nlm.nih.gov/pubmed/28379488
2) If can, how should I set the platform (PL) information in Read Group (RG)? Because I have noticed that the valid values of PL are just ILLUMINA, SOLID, LS454, HELICOS and PACBIO.
Thanks very much!

Issue · Github
by Sheila

Issue Number
3048
State
closed
Last Updated
Assignee
Array
Closed By
chandrans

Best Answers

  • SheilaSheila Broad Institute admin
    Accepted Answer

    @jiykun
    Hi again,

    It seems you should ask for a PL value (like BGI) to be added in HTS-SPEC. Our team cannot add it for you.

    -Sheila

Answers

  • ymcymc Member

    While I never looked at BGISEQ data, since GATK can work with the four bogus q-scores generated by NovaSeq, I think it should work as well.

  • @Sheila
    Hi Sheila,
    Thanks for your reply.
    1) They are Phred Scaled scores in BGISEQ data.
    2) Did you mean that the PL can be spcified as any one of the valid values, and the PL information will not affect BQSR? Then why does BQSR program check the PL value in my data?
    Thanks!

  • SheilaSheila Broad InstituteMember, Broadie admin
    edited April 2018

    @jiykun
    Hi,

    1) I think in that case, there should be no issue.

    2) I am not 100% certain, but it could be a way of record keeping for yourself. In this case, you know the PL is BGIseq, but for testing purposes, can you try a different value?

    Thanks,
    Sheila

  • SheilaSheila Broad InstituteMember, Broadie admin
    Accepted Answer

    @jiykun
    Hi again,

    It seems you should ask for a PL value (like BGI) to be added in HTS-SPEC. Our team cannot add it for you.

    -Sheila

  • jiykunjiykun Member

    @Sheila said:
    @jiykun
    Hi again,

    It seems you should ask for a PL value (like BGI) to be added in HTS-SPEC. Our team cannot add it for you.

    -Sheila

    Thanks!

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