single mode vs paired mode

[melodysyue]

I ran variant calling for a cfDNA in Vardict in the single mode. Then later on, I sequenced the matched germline and reran variant calling for the same cfDNA in the paired mode. Out of curiosity, I also called variants in the matched germline sample using the single mode.

I thought the list of variants in the raw vcf file generated in the paired mode = union (variants of cfdna in the single mode and variants of germline in the single mode). However, it is not the case. There are thousands of variants that were uniquely called in the single mode, but not in the paired mode, and vice versa. Just to be clear, the comparison was done on the raw vcf outputs from Vardict without any filtering.

Could you help me explain the discrepancy?

Thanks,
Yue