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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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CSQ annotation - should be frameshift #2212

Closed JakeHagen closed 3 months ago

JakeHagen commented 3 months ago

Hello

I annotated this variant chr7-74711106-CAAG-CT with bcftools csq v1.20. For all transcripts it is giving me inframe_deletion&splice_region as the consequence. I think this should be a frameshift variant. Is there something I am not understanding, or could this be a bug?

Thank you Jake

pd3 commented 3 months ago

At a cursory glance yes, however it really depends on the sequence context and the gene model. More information is needed to debug this. Can you share a small test case to reproduce the problem please? It can be created for example like this

/path/to/bcftools-dir/test/csq/make-csq-test -f ref.fa -g genes.gff -o test -p  74711106-CAAG-CT -t TRANSCRIPT_ID
JakeHagen commented 3 months ago

Thank you for looking at this. Attached is the test case created with the command

../bcftools-1.20/test/csq/make-csq-test -f ./genome.hg38rg.fa -g ./ensembl/Homo_sapiens.GRCh38.112.gff3.gz -o test -p 74711106-CAAG-CT -t ENST00000573035

bcftools_csq_test_7-74711106-CAAG-CT.tar.gz

pd3 commented 3 months ago

Thank you for the test case. I can confirm this was a bug, and it should be fixed now by https://github.com/samtools/bcftools/commit/a05480ccc32a4ab5dd9b7a732040f9f9f5742a24, please try it out

JakeHagen commented 3 months ago

Yep it is now being reported as frameshift&splice_region Thank you