WGS tumor-only samples allele frequency

Question

[noemichael]

We have tumor-only WGS data...

I did allignment with the GATK pipeline. After that, I did variant calling with SamTools. This gives me a VCF file with in the INFO-column, the DP4 (giving me the amount of reads (both forward and reverse) with the reference sequence and the amount of reads (both forward and reverse) with the alternative sequence).

I wanted to make an allele frequency scatter, to search for large areas of CNA or LOH... However, CNVkit does not accept it like this. Is there an uncomplicated way to get a SNP-array / allele frequency scatter from WGS?