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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

Food for thought: rank STR expansion variants? #84

Closed dnil closed 2 years ago

dnil commented 6 years ago

Allow genmod to rank STR expansion variants; e.g. an expansionHunter vcf:

fileformat=VCFv4.1

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

ALT=

ALT=

X 146993568 . G , . PASS END=146993628;REF=20;RL=60;RU=CGG;REPID=FMR1 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR 1/2:SPANNING/INREPEAT:30/125:30-30/100-147:3/0:20/21:0/33

Would then need the knowledge that normal variants in FMR1 go up to "STR65".. Or just pass them through to visualisation anyway?

dnil commented 2 years ago

We kind of solved this with Stranger. Closing this and continuing there.