SAGE: multiallelic variants

hartwigmedical / hmftools

Various algorithms for analysing genomics data

GNU General Public License v3.0

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SAGE: multiallelic variants #468

Closed andrianovam closed 4 months ago

andrianovam commented 9 months ago

Could you please clarify how SAGE is dealing with multiallelic variants (positions with more then one alternative allele) and how such variants should be outputted (each alternative allele as a separate line/all alt alleles separated by coma in one line/etc)? I am sorry if I missed this but I was not able to find answer in the documentation..Thank you!

charlesshale commented 9 months ago

Sage will write these as separate lines in the VCF