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Created 2015-08-31 11:58:59 | Updated | Tags: baserecalibrator best-practices ploidy pooling
Comments (3)

Dear GATK Team,

baserecalibrator is in the newest Best Practices recommendations. Does this tool support or would you recommend it's usage for samples with ploidy higher then 2 (e.g. pooled samples)?

Thanks! Bernt


Created 2013-01-09 11:16:39 | Updated 2013-01-09 11:17:10 | Tags: exome pooling lanes
Comments (2)

Hi,

I have exome data run on two lanes per library is it better to combine the lanes into one or to run each lane independently through GATK? What are the pros and cons? Many thanks