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Old 02-04-2012, 05:07 AM   #3
krawitz
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Location: Bonn

Join Date: Feb 2010
Posts: 30
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the samtools mpileup output can be piped into VarScan to apply a coverage and frequency filter:
samtools pileup -f reference.fasta myData.bam | java -jar VarScan.v2.2.jar pileup2snp --min-coverage 20 --min-var-freq 0.14
see: http://varscan.sourceforge.net/using-varscan.html
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