Closed zeliasoo closed 2 years ago
Hi, can you try with the latest version (v0.2.7) of slivar and see if that resolves it? If not, we can debug further if you can send the full command that you ran.
Hi Brent, sorry I only just saw this. When I tried to run 0.2.7, it has a slightly different error message and stops at the same stage of running.
Command error:
> slivar version: 0.2.7 71af7d12881ae0590c6d2a97ef2b282cc93fe7c6
[slivar] no ped file specified, not able to determine family relationships.
warning: unknown impact "@17397477" from csq "@17397477" please report the variant at https://github.com/brentp/slivar/issues
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
Hope you can help
Hi, this is because of the way that you ran bcftools CSQ the @17397477
is a reference to another entry. You'll need to run bcftool csq something like this:
bcftools csq -s - --ncsq 40 -g $gff -l -f $fasta $vcf -O u -o $vcf_with_csq
While trying to run slivar v0.2.4, we encountered the following error:
Command error:
We run slivar in our bioinformatic pipeline and everything goes smoothly, but filtered list to tsv part failed and we can't solve it. Can anyone help us solve this?