zaka-edd

Feature Request: Add --partition-tag option to "modkit extract calls"

2

Currently, the ```--partition-tag``` option is available for the ```modkit pileup``` command, allowing users to partition output into multiple bedMethyl files based on tag-value pairs. It would be beneficial to have...

Coordinate <= 0 detected. Did you forget to use the -0 option?

1

Hi, I am trying to use Spectre but I keep getting this error ``` spectre::2025-03-14 14:34:43,092::INFO::spectre.spectre> Spectre input: CNVCaller --coverage /home/zeddafir/LRS-CNV-calling/EP2086.08/EP2086.08.regions.bed.gz --sample-id EP2086 --output-dir output/ --reference /net/mergefs/mergefs/complgen/refseq/hg38/genome_hg38.ifas --blacklist /home/zeddafir/LRS-CNV-calling/Spectre/data/grch38_blacklist_spectre.bed --min-cnv-len...

Change name of sample in SNF file

4

Hi, Thank you for providing sniffles2. I was wondering if it is possible to change the sample name for a SNF file? I tried changing the name of the `.snf`...

When running Sniffles2, I noticed that BND structural variant calls are being reported with 0-based coordinates instead of the expected 1-based VCF standard. For example: ``` chr21 24015867 Sniffles2.BND.4M26D N...