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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
The text was updated successfully, but these errors were encountered:
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.
Hello, does
bcftools csq
support multi nucleotide variants?This MNV
1-201363379-CC-AA
produces the CSQ below when run in local modeIt 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
The text was updated successfully, but these errors were encountered: