Multi allelic VCFs - ACEnglish/truvari GitHub Wiki
Truvari only compares the first alternate allele in VCFs. If a VCF contains multi-allelic sites such as:
chr2 1948201 . T TACAACACGTACGATCAGTAGAC,TCAACACACAACACGTACGATCAGTAGAC ....
Then pre-process the VCFs with bcftools:
bcftools norm -m-any base_calls.vcf.gz | bgzip > base_calls_split.vcf.gz