SEQanswers - View Single Post - A heretically simple approach to variant calling

krawitz · 02-04-2012, 05:07 AM

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

02-04-2012, 05:07 AM	#3
krawitz Member Location: Bonn Join Date: Feb 2010 Posts: 30	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