Error: bcftools csq --- splice_build_hap: Assertion `splice->tr->beg <= rbeg' failed.

[sbgonenc]

Hi bcftools team!

I come across to splice_build_hap: Assertion `splice->tr->beg <= rbeg' failed. error while annotating my vcf. The vcf line that produces this error is the following:

chr9	19518750	.	CA	C	23.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:6:3:0,3:1:22,4,0

and the location overlaps with these records in the ensembl gff:

9       ensembl exon    19518746        19518750        .       +       .       Parent=transcript:ENSCAFT00000047742;Name=ENSCAFE00000400429;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=ENSCAFE00000400429;rank=1;version=1
9       ensembl CDS     19518746        19518750        .       +       0       ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069

Here is the full command I have used:

bcftools csq \
                 --fasta-ref chr9.fasta.gz \
                 --gff-annot chr9.gff \                 
                 --phase a  \
                 --unify-chr-names 1 \
                 --threads 4  \
                 -O z chr9_test.vcf  \
                 -o chr9_annotated.vcf.gz  \
                 --write-index=tbi

I also upload the files needed to replicate this error:

bcftools_csq_case.zip

I am more than happy to provide any details you may need, also open to suggestions on how to circumvent this problem.

Cheers!