Jonas Andreas Sibbesen

Hi Prithika, This error arises when there is no kmers available to estimate the parameters for the negative binomial genomic kmer count distribution for each sample. These parameters are estimated...

That is strange. I would have expected it to work using the smaller variant set. Would it be possible for you to share with me the smaller variant set and...

Glad to hear that it works now. Please let me know if you run into any other issues.

That is weird. Did you remember to convert the symbolic alleles in the input vcf to sequences before running *cluster*? You can do this using `bayesTyperTools convertAllele`. If that is...

It looks like you have a lot of zero-inflation in your k-mer counts (see the high estimated variance). This also results in a lot of the genotypes being filtered due...

Come to think about it. Incorrect SV breakpoints could also result in inflated zero count kmers. Do you see that more deletions are filtered compared to insertions? However, that would...

BayesTyper does not perform well when the breakpoints are not exact due to its use of exact matching kmers. If you can you share the latest results then I will...

Thanks, I am happy to help. Would it be possible to also share the log files (stdout) from BayesTyper?

@Parsoa I have looked at the results and most of the remaining filtered genotypes are due to a low genotype posterior probability (GPP). By default BayesTyper filters all genotypes with...

Hi Martin, I am currently working on a new version that I hope to release later this week that specifically adresses the issue you mention. In the new release all...