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xml_to_bas.pl - detect readgroup id clashes and attempt to reconcile #54

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keiranmraine opened this issue Dec 15, 2014 · 1 comment
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xml_to_bas.pl - detect readgroup id clashes and attempt to reconcile #54

keiranmraine opened this issue Dec 15, 2014 · 1 comment
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If ID field of RG header is not unique within the sample prior to merging it is modified during the merge step. In most cases in PanCancer this can be resolved by correlating on PU tag instead.

Example of bad XML:

https://gtrepo-ebi.annailabs.com/cghub/metadata/analysisFull/0d8605fc-6510-4b3d-91e9-11c7c771d2f3
@keiranmraine keiranmraine self-assigned this Dec 15, 2014
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Mini BAM to test this against included as t/data/reconcile_bas.bam

keiranmraine added a commit that referenced this issue Dec 15, 2014
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Merge pull request #55 from ICGC-TCGA-PanCancer/bas_compensate
648b497 
Resolves #54
@keiranmraine keiranmraine mentioned this issue Dec 15, 2014
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keiranmraine added a commit that referenced this issue Dec 15, 2014
@keiranmraine
Merge pull request #56 from ICGC-TCGA-PanCancer/dev
7cb9d0a 
Resolves #54
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