I have a whole-genome sequencing data from Illumina company. The SNPs number I called using samtools/pileup, samtools/mpileup and SNVMix is 3,752,858, 3,959,353, and 5,836,045 for tumor sample, respectively. The corresponding SNPs number for blood sample is 3,512,896, 3,686,117, and 5,456,739.
It have been said that samtools/mpileup is better than samtool/pileup (for single-sample SNP calling, they differ little), and SNVMix is suitable especially for cancer sequencing. So the SNPs number from SNVMix should be less than samtools/mpileup, and samtools/mpileup should be less than samtools/pileup.
Why here the number of SNPs from samtools/pileup < samtools/mpileup < SNVMix? Do the SNPs number have any problems here? Thanks.