I am using Varscan 2.2.11 to analyze a tumor-normal pair of whole exome NGS data. I used 1000genomes reference genome (from here) and my .bam files are sorted. I use shell script similar to this to call VarScan and get the following summary after my run:
2 015 987 104 positions in tumor 2 015 519 315 positions shared in normal 90 913 571 had sufficient coverage for comparison 0 were called Reference 496 were mixed SNP-indel calls and filtered 90 834 408 were called Germline 0 were called LOH 0 were called Somatic 78667 were called Unknown 0 were called Variant
Obviously, there are some problems, since almost all positions with sufficient coverage are called Germline and none are called Reference. Can you point out what am I doing wrong, please.