Aliz Rao

I tried running VarScan 2.3.9 on a 2-sample mpileup file using the following command: java -jar $D/varscan_2.3.9/VarScan.v2.3.9.jar somatic $BAM/${tumor}${normal}.mpileup $VCF/${tumor}${normal}.varscan --mpileup 1 In my output file, the genotype columns normal_gt and tumor_gt contain letters instead of the expected 0/1, 1/1, etc. Do you know what could be going on? How do I interpret the letters? Example: chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2...

I tried running VarScan 2.3.9 on a 2-sample mpileup file using the following command: java -jar /home/arao/apps/varscan_2.3.9/VarScan.v2.3.9.jar somatic $BAM/${tumor}${normal}.mpileup $VCF/${tumor}${normal}.varscan --mpileup 1 In my output file, the genotype columns normal_gt and tumor_gt contain letters instead of the expected 0/1, 1/1, etc. Do you know what could be going on? How do I interpret the letters? Example: chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1...