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adds a barcode option to FastqToBam #936

Merged
merged 5 commits into from
Sep 11, 2023
Merged

adds a barcode option to FastqToBam #936

merged 5 commits into from
Sep 11, 2023

Commits on Sep 9, 2023

  1. minor doc fix, platform unit does not relate to sample barcode 

    re fulcrumgenomics#935
    @bwlang
    bwlang committed Sep 9, 2023
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  2. adds a barcode option to FastqToBam 

    fixes fulcrumgenomics#935
    @bwlang
    bwlang committed Sep 9, 2023
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Commits on Sep 10, 2023

  1. Revert "minor doc fix, platform unit does not relate to sample barcode" 

    This reverts commit b960886.

GATK seems to want a sample-barcode in there too

>PU = Platform Unit
>The PU holds three types of information, the {FLOWCELL_BARCODE}.{LANE}.{SAMPLE_BARCODE}. The {FLOWCELL_BARCODE} refers to the unique identifier for a particular flow cell. The {LANE} indicates the lane of the flow cell and the {SAMPLE_BARCODE} is a sample/library-specific identifier. Although the PU is not required by GATK but takes precedence over ID for base recalibration if it is present. In the example shown earlier, two read group fields, ID and PU, appropriately differentiate flow cell lane, marked by .2, a factor that contributes to batch effects.
>(https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups)
    @bwlang
    bwlang committed Sep 10, 2023
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Commits on Sep 11, 2023

  1. a list as suggested

    @bwlang
    bwlang committed Sep 11, 2023
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  2. switches back to a single string for input

    @bwlang
    bwlang committed Sep 11, 2023
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