Groza Cristian

Here is an example if it helps. It contains a 6kb insertion surrounded by 4kbp flanks and I wish to map it to a reference region that is 8kbp long....

Also, if it helps, here is the dotplot with the target region (y-axis) and the contig with the insertion (x-axis). As we can see, there is a large gap in...

Hi, I am experiencing the same issues. I am using the 1KGP dataset as the reference, and somalier labels most of my samples as AMR. I have been using 5...

Any progress on this issue? I am trying to use graph aligner to perform gapped alignment of long reads and then augment the graph with the insertions. I know I...

I moved that code into my own source files and the symbol is found. Seems to me there is something wrong with the way the library is compiled?

Hi, Thank you for giving our pipeline a try. I think the fastest way to integrate minigraph-cactus into our pipeline is by running vg deconstruct on the minigraph-cactus graph, and...

As an update, we just successfully processed HPRC with GraffiTE from the VCF obtained by decomposing the pangenome. So an approach where we decompose the minigraph-cactus VCF, filter it for...

To truly handle COMPLEX variants, we would need to spell the alleles into sequences by following their paths through the genome graph bubbles, run these through repeat masker and then...

Hi The argument is not being passed to minimap2. It's nextflow trying to invoke singularity with that parameter and getting an error. You might need to check your singularity version...

Seems that bcftools is picking up an environmental variable, and trying to use that as a temporary directory inside the container where it's not mounted. Try adding `--cleanenv` after `--contain`...