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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
74 stars 18 forks source link

Automatically determine pedigree? #89

Closed santiagorevale closed 5 years ago

santiagorevale commented 5 years ago

Hi guys,

I usually have to deal with family samples that have been mixed up, so the relationship between them has been lost (which one is the father, mother, children, siblings, etc).

I'm not sure if I'm getting right or wrong but, is it possible with genmod to determine the relationship of the samples based on a multi-sample VCF file? If possible, could you show me how?

Thank you very much in advance.

Cheers, Santiago

moonso commented 5 years ago

Hi Santiago, at the moment it is not possible with genmod. You could try to do something with https://github.com/moonso/variant_integrity or preferably https://github.com/brentp/peddy