Karoliina Salenius

Hi, many thanks for your work with slivar and smoove! Quick question on this topic, I'm running slivar with docker and the above fix (SLIVAR_IMPACTFUL_ORDER=/path/to/adjusted-order.txt slivar expr ...) throws an...

`head $SLIVAR_IMPACTFUL_ORDER ` `transcript_ablation` `splice_acceptor` `splice_donor` `stop_gained` `...` I tested running the container with `docker run --name="slivar" -v "/mnt:/mnt" -e $SLIVAR_IMPACTFUL_ORDER --cpus "8" -dt "brentp/slivar"` But get the same warnings...

Hi, thanks! Here's the beginning of the log: `> slivar version: 0.2.7 71af7d12881ae0590c6d2a97ef2b282cc93fe7c6` `[slivar] 4 samples matched in VCF and PED to be evaluated` `[slivar] message for /mnt/gemma/bin/resources/slivar/gnomad.hg38.genomes.v3.fix.zip:` ` >...

Sorry, I was just re-reading back in the thread and notice you mention not having all the consequences (as these are probably quite low impact) in the list is not...

Thanks for your insights and the great the tool! I will modify the script for my hifi data. It's low coverage (~10X) and I appreciate it's not optimal for hla...

Hi, I'm reopening the issue although I'm not sure whether my question falls under the same category, but likely it has something to do with alignment. I managed to genotype...

Hi, thanks for the insights! I have been observing the alignment files outputted by specHLA (DPB1.bam), and the read quality and mapping seem fine to me. I have long read...

Right, first of all, it's great to have all the outputs for troubleshooting! Seems that there's a lot going on under the hood. So for most of the samples, the...

Wow, great, thank you for your trouble! Interesting, that there is an identical sequence in BAC and DPB1. I will test blast, and am currently downloading the databases as my...

Hi, after blasting a number of the dubious reads, they do hit some kind of BACs, though with slightly different id than in your screenshot. I tried running HiFiAdapterfilt but...