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Copy pathRunVarscan
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RunVarscan
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#!/bin/sh
ref=$1
varscanjar=$2
samplelist=$3
outputfile=$4
# bams=$*
# echo $ref
# echo $bams
# echo $outputfile
# echo $varscanjar
shift
shift
shift
shift
# echo "samtools mpileup -f $ref $* | java -jar $varscanjar mpileup2snp --p-value 99e-02 --strand-filter 1 --output-vcf 1 > $outputfile"
#samtools mpileup -f $ref $* | java -jar $varscanjar mpileup2snp --p-value 99e-02 --strand-filter 1 --output-vcf 1 --vcf-sample-list $samplelist > $outputfile
samtools mpileup -f $ref $* | ~/Programs/Java/jre1.7.0_45/bin/java -jar $varscanjar mpileup2snp --p-value 0.10 --strand-filter 1 --output-vcf 1 --vcf-sample-list $samplelist > $outputfile
#echo "samtools mpileup -f $ref $* | java -jar $varscanjar mpileup2snp --p-value 0.10 --strand-filter 1 --output-vcf 1 --vcf-sample-list $samplelist > $outputfile"
# samtools mpileup -f $ref $* | java -jar $varscanjar mpileup2snp --p-value 99e-02 --strand-filter 1 --output-vcf 1 --vcf-sample-list $samplelist > $outputfile
# samtools mpileup -f $ref $bams | java -jar $varscanjar mpileup2snp --p-value 99e-02 --strand-filter 1 --output-vcf 1 > $outputfile