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  • remove duplicates in markduplicates

    If I was going to view a bam file in IGV both with duplicayes marked and then after they are removed are these commands accurate:

    Flag duplicates in BAM
    Code:
    java -jar picard.jar MarkDuplicates \ 
        INPUT=sorted_reads.bam \ 
        OUTPUT=dedup_reads.bam \
        METRICS_FILE=metrics.txt
    Remove duplicates from BAM
    Code:
    java -jar picard.jar MarkDuplicates \ 
        INPUT=sorted_reads.bam \ 
        OUTPUT=dedup_reads.bam \
        REMOVE_DUPLICATES=true \
        METRICS_FILE=metrics.txt
    Are there additional options to use?

    Thank you .

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