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

Join Date: Oct 2011
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Question "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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