How do I prepare VCF files generated by DRAGEN MANTA to be used as input for Emedgene?

All variant types (ie. SNV/indel, CNV, SV, STR) ingested into the Emedgene platform require separate vcf files. In order to ingest a Dragen Manta vcf for Dragen version < 4.2, the following line should be replaced within the header of the Dragen Manta vcf:

Replace

##source=DRAGEN <version>

by

##source=MANTA-DRAGEN <version>

Example:

Replace

##source=DRAGEN 05.121.645.4.0.3

by

##source=MANTA-DRAGEN 05.121.645.4.0.3

Note:

Variant types currently annotated and displayed in Emedgene are DEL, DUP and INS.