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Old 03-05-2012, 07:43 AM   #1
Location: US

Join Date: Oct 2011
Posts: 47
Question "Bcftools mpileup" removes marked duplicates?


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 "


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

Thanks very much
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