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  • angerusso
    Member
    • Oct 2011
    • 47

    "Bcftools mpileup" removes marked duplicates?

    Hey,

    My question is does samtools mpileup automatically removed duplicates from test.marked.bam output from Picard/MarkDuplicates?

    I used Picard Tools to create: test.marked.bam

    Then I use
    "samtools mpileup -uf test.marked.bam | bcftools view -bvcg -> test.marked.bcf "

    and

    "bcftools view test.marked.bcf | vcfutils.pl varfilter -D1000 >test.marked.vcf"

    Thanks very much

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