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MarkDuplicates on reads with different lengths

SvyatoslavSidorovSvyatoslavSidorov St. Petersburg, RussiaMember

Dear GATK team,

Am I right that since MarkDuplicates considers only 5' coordinates of reads, it should work properly on reads (both paired-end and single-end) that have different lengths (due to quality trimming from 3')?

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Answers

  • SvyatoslavSidorovSvyatoslavSidorov St. Petersburg, RussiaMember

    Geraldine, thank you very much!

  • SvyatoslavSidorovSvyatoslavSidorov St. Petersburg, RussiaMember
    edited April 2016

    @jalves and @Geraldine_VdAuwera, thanks for your corrections!

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