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  • Duplicates removal on analysis-ready bam file with duplicates marked

    Hi pals,
    I have already preprocessed bam file that has duplicates marked, realigned and BQSR performed by GATK.
    Because of some reasons, I need to remove the duplicates.

    Is it a good idea to remove duplicates on the analysis ready bam file, rather than repeating entire preprocessing with duplicates removal ?

    If I remove the duplicates from analysis-ready bam, will it be necessary to perform realignment and BQSR again ?

    Thanks

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