Script to calculate alt allele freqs at given VCF positions

[etal]

Since Mutect2 is a frequently used somatic SNV caller and cannot be made to report germline SNPs in the tumor sample, users are frequently stuck trying to use CNVkit's VCF features to detect allelic imbalance etc. (e.g. #184, #195).

It would be sufficient to just use samtools or similar to calculate the ALT allele frequency at a bunch of given SNP sites, e.g. dbSNP v.129, 1000 Genomes "omni" sites, a matched normal sample's germline calls, or really any normal sample's SNP VCF. The command to do that is not entirely obvious, so let's provide a script that does it properly.

Also, ensure that CNVkit's handling of that output VCF is as expected.