Claire Mérot

Thanks a lot to all of you for the answers and advice. If I understood correctly, this is much simpler than I felt! Thanks for the guidance For analysis 1,...

True, vg paths -Lv 09_vgiraffe/vcf_graph/vcf_graph_giraffe_converted.xg (produced by vg convert) gives me nothing while vg paths -Lv 09_vgiraffe/vcf_graph/vcf_graph_giraffe.xg (produced with -R XG argument) gives me the list of Chromosomes in the...

As a feedback the pipeline (vg autoindex --workflow giraffe -R XG ; vg giraffe; vg pack; vg call ), is giving very promising results. I am now expanding to more...

Hi, I don't know why I can't see the thread on github but the short answer is that you define snarls and you ask it to genotype all variants if...

Thanks for your reply, And thanks a lot the addition in the readme about SV-calling with minigraph, I'm trying that, as I have two assemblies to compare! I was wondering...

Thanks for the fast reply. Yes, I'd be very interested when this is implemented, I'll be following your updates. We are looking for rearrangements (inversions, fusions, etc), and LD can...

Thanks to both of you for your answers. Hannes, you are right, a few of them did indeed have a "PASS" although that was very rare. I'll give it a...

Hello, Thanks for the samplot development, it is very useful! It works super well for deletion. I'd be very interested if something is developed to extend the feature to insertions...

hi Mahul, thanks for your answer. These are the lines of codes I used (so no -maxmatch, should I?) #run nucmer nucmer -t $NB_CPU \ "$INPUT_FOLDER"/"$REFERENCE" "$INPUT_FOLDER"/"$QUERY" \ -p "$OUTPUT_FOLDER"/sam2ref...