Is it possible to output an vcf with clinical annotation?
Opened this issue · 1 comments
For example, straglr can add annotation to an vcf output with pathogenic_min and then call whether it is full_mutation, pre_mutation or normal, e.g.
chr21 43776443 . G . PASS SVTYPE=STR;END=43776479;REF=5;RL=36;RU=GGGGCGC;REPID=CSTB;VARID=CSTB;STR_STATUS=pre_mutation;STR_NORMAL_MAX=3;STR_PATHOLOGIC_MIN=30;RankScore=1:20;HGNCId=2482;InheritanceMode=AR;DisplayRU=CCCCGCCCCGCG;SourceDisplay=GeneReviews_Internet_2019-11-07;Source=GeneReviews;SourceId=NBK535148;Disease=EPM1 GT:SO:CN:CI:AD_SP:AD_FL:AD_IR 1/1:SPANNING/SPANNING:4/4:4-4/4-4:12.5/12.5:0/0:0/0
chr14 23321472 . G , . PASS SVTYPE=STR;END=23321490;REF=6;RL=18;RU=GCG;REPID=PABPN1;VARID=PABPN1;STR_STATUS=full_mutation,normal;STR_NORMAL_MAX=10;STR_PATHOLOGIC_MIN=11;RankScore=1:30;HGNCId=8565;InheritanceMode=AD;DisplayRU=GCN;SourceDisplay=GeneReviews_Internet_2020-10-22;Source=GeneReviews;SourceId=NBK1126;Disease=OPMD GT:SO:CN:CI:AD_SP:AD_FL:AD_IR 1/2:SPANNING/SPANNING:16/6:16-16/5-6:1/31:0/0:0/0
Sure. I will add this function in the next release. Thanks for the suggestion!
Li