cmccabe

Thank you very much.... that fixed it :).

I am using varscan 2.3.9 and getting the below error: java -jar /home/cmccabe/Desktop/NGS/VarScan.v2.3.9.jar trio trio.mpileup trio.mpileup.output \ --min-coverage 10 --min-var-freq 0.20 --p-value 0.05 \ -adj-var-freq 0.05 -adj-p-value 0.15 SNPs will be output to trio.mpileup.output.snp.vcf Indels will be output to trio.mpileup.output.indel.vcf Min coverage: 20 Min reads2: 4 Min var freq: 0.2 Min avg qual: 15 P-value thresh: 0.05 Adj. min reads2: 2 Adj. var freq: 0.05 Adj. p-value: 0.15 Reading input...