MNV consequence annotation in local mode

[JakeHagen]

Hello, does bcftools csq support multi nucleotide variants?

This MNV 1-201363379-CC-AA produces the CSQ below when run in local mode

missense|TNNT2|ENST00000660295|protein_coding|-|162EE>162D*|201363379CC>AA,missense|TNNT2|ENST00000236918|protein_coding|-|172EE>172D*|201363379CC>AA,missense|TNNT2|ENST00000360372|protein_coding|-|132EE>132D*|201363379CC>AA,missense|TNNT2|ENST00000367317|protein_coding|-|157EE>157D*|201363379CC>AA,missense|TNNT2|ENST00000367318|protein_coding|-|162EE>162D*|201363379CC>AA,missense|TNNT2|ENST00000422165|protein_coding|-|172EE>172D*|201363379CC>AA,missense|TNNT2|ENST00000656932|protein_coding|-|172EE>172D*|201363379CC>AA,missense|TNNT2|ENST00000367322|protein_coding|-|161EE>161D*|201363379CC>AA,missense|TNNT2|ENST00000666449|NMD|-|162EE>162D*|201363379CC>AA,missense|TNNT2|ENST00000658476|protein_coding|-|162EE>162D*|201363379CC>AA,missense|TNNT2|ENST00000412633|protein_coding|-|162EE>162D*|201363379CC>AA,missense|TNNT2|ENST00000367320|protein_coding|-|132EE>132D*|201363379CC>AA,missense|TNNT2|ENST00000509001|protein_coding|-|162EE>162D*|201363379CC>AA,missense|TNNT2|ENST00000438742|protein_coding|-|156EE>156D*|201363379CC>AA,missense|TNNT2|ENST00000455702|protein_coding|-|167EE>167D*|201363379CC>AA,3_prime_utr|TNNT2|ENST00000663843|NMD

It looks like the amino acid change and DNA change is correct, but it would be nice if the consequence would have the more impactful consequence between the missense and the stop gain or maybe use the &.

This was using bcftools 1.16 and this was the command
csq -l -f ./genome.hg38rg.fa -g ./Homo_sapiens.GRCh38.107.gff3.gz ./test.vcf

Thanks
Jake

[pd3]

If the MNV is in a single VCF record, there should be no difference between the local mode and the haplotype-aware mode. The latter impacts only variants present in seperate VCF records.

This indeed is a bug, both modes should have reported stop_gained. This is now fixed, thank you for the bug report.

[JakeHagen]

Wow that was quick. Thanks a lot