Guillaume Barreau

NullPointerException on stats.sh

Hello, I have used varscan with java -jar VarScan.v2.3.9.jar mpileup2cns RS.pileup --vcf-sample-list sample.list --min-reads2 3 --min-coverage 15 --p-value 0.9 --strand-filter 0 --variants --output-vcf > RS.vcf The vcf file is attached to this message. When I look at the results, I see that there is a field called AD (allele depth), a field called DP and a field called FREQ. In most cases, FREQ = AD/DP. However in some cases, this doesn't seem to be the case. Furthermore in those cases, I can't see...