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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Running exomiser on vcf with multiple probands and multi family ped #574

Open vinoekat opened 1 month ago

vinoekat commented 1 month ago

Hello Exomiser team! Can Exomiser be run on multi-family VCF (not just multi sample, but many different probands and parents)? I have a VCF file with 31 trios (mother, father, child) and a matching Ped file. Can I analyze all of them in one run? If so, how should I specify probands in the yml file? As a list of strings?
Thank you.

nlharris commented 1 day ago

@julesjacobsen can you answer this question when you get a chance? Thanks!

julesjacobsen commented 1 day ago

Hi @vinoekat, sorry about the late reply. Exomiser will only analyse a single proband at a time, so you'll need to run it for each proband separately. You should also split the VCF and PED file into individual families as the pedigree tool will probably not handle VCF genotypes for this correctly.