I have VCF files from Illumina Dragen Enrichment where the variant calling was performed after sequencing using illummina. The experimental design was set up to compare the tumor with normal (there was no control). The output VCF I have consists of both somatic and germline variants. My goal would be to filter out the Germline Variant and get the somatic variants only in the final VCF file. I know this is not what the GATK pipelines recomended but I also want to test this and see if the result would be similar (consistent) with the results from GATK pipelines. 

I was wondering if I can use tools from GATK workflow and used my VCF files and know common variants from repositories (like 1000 genome project) to carry this out.

Any advise would be appreciated.

Thanks!

Seke

REQUIRED for all errors and issues:
a) GATK version used: GATK 4.3
b) Exact command used: Not abailable
c) Entire program log: Not available