Describe the issue
A question about annotation of mutation types, i can`t understand why the annotation tag is frameshift_variant and the same time also is synonymous_variant, like this, frameshift_variant&synonymous_variant
To Reproduce
- SnpEff version: 5.2e
- Genome version:GRCh37.p13
- SnpEff full command line:
- Output / Error message: java -Xmx4g -jar snpEff.jar GRCh37.p13 examples/test.vcf > test.ann.vcf
Expected behavior
1 120458463 . TAT AA . PASS ADP=221;SBR=73:176:1:1;DCS=0;ANN=AA|frameshift_variant&synonymous_variant|HIGH|NOTCH2|NOTCH2|transcript|NM_024408.4|protein_coding|34/34|c.6880_6882delATAinsTT|p.Ile2294fs|7138/11425|6880/7416|2294/2471||;LOF=(NOTCH2|NOTCH2|2|0.50) GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:::135:133:2:1.48148%:0.2490706319702765:::53:80:0:2
Data
1 120458463 . TAT AA . PASS ADP=221;SBR=73:176:1:1;DCS=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:::135:133:2:1.48148%:0.2490706319702765:::53:80:0:2
Describe the issue
A question about annotation of mutation types, i can`t understand why the annotation tag is frameshift_variant and the same time also is synonymous_variant, like this, frameshift_variant&synonymous_variant
To Reproduce
Expected behavior
1 120458463 . TAT AA . PASS ADP=221;SBR=73:176:1:1;DCS=0;ANN=AA|frameshift_variant&synonymous_variant|HIGH|NOTCH2|NOTCH2|transcript|NM_024408.4|protein_coding|34/34|c.6880_6882delATAinsTT|p.Ile2294fs|7138/11425|6880/7416|2294/2471||;LOF=(NOTCH2|NOTCH2|2|0.50) GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:::135:133:2:1.48148%:0.2490706319702765:::53:80:0:2
Data
1 120458463 . TAT AA . PASS ADP=221;SBR=73:176:1:1;DCS=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:::135:133:2:1.48148%:0.2490706319702765:::53:80:0:2