The usage of the software is: verifyBamID --vcf [input.vcf] --bam [input.bam] --out [output.prefix] --verbose --ignoreRG

I am reading the manual, but it is still not clear to me. (1) Should I run the command once for each pair of samples? (2) should the .vcf file the list of germline mutations from normal sample? Can I get this from MuTect output, and get a list of mutations that are rejected? (3) Should the .bam file be from the matched tumor sample?

Thank you very much in advance.