Duda5

no plottable samples with matched alignment files

5

I generated a `vcf` file with `sniffles` (on PacBio HiFi reads aligned to hg38) and I am trying to visualize SVs using `samplot vcf` (`conda` installation). `vcf` file stats: ```...

pipeline crashed : scaffold (Scaffold graph is inconsistent)

1

Hi, I only managed to run `gapless` on my ONT assembly (~400 contigs, haploid genome size of 3.1Gbp, there are no gaps in contigs) up to `gapless.py scaffold` stage in...

samtools ampliconclip takes quality scores from read start rather than specifed region

1

Package versions (compiled on Ubuntu 22.04.4 LTS x86_64): ``` samtools 1.19.2-11-g15d6538 htslib 1.19.1-19-g5d2c3f72 ``` I am trying to extract read fragments and their quality scores from a specific region of...