Is there any software designed for the VCF file similarity search? Or the software for WGS similarity search using .bam/.sam and fastq files?
BEDtools can be used to compare VCFs and identify the common and unique variants between files.
Thx, what functions to use and could you show a case example of data processing?
The 'intersect' command gives the common variants, and 'subtract' the unique ones. Examples of command usage are shown at the BEDtools link I provided.