tnguyengel

Has the feature to split up SNF files by chromosome already been released? If so, where can we find the new binaries?

I noticed that there is a new release: https://github.com/fritzsedlazeck/Sniffles/releases/tag/v2.3.2. Does this happen to solve this issue of large RAM usage for many samples? (We estimated Sniffles v2.2. will use up...

> Whats the command you've been trying to run sniffles with? For both Sniffles v2.3.2 and Sniffles v2.2, we were running `sniffles -t ${threads} --allow-overwrite --input "${snf_list}" --vcf "${out_merged_vcf}"` >...

We don't have the full 5000 samples to run yet, but that will be the final set that we eventually run with. We will rerun scaling tests with v2.3.3, and...

Thanks! That sounds like a quick workaround! From brief googling, a human gene has ~4 transcripts on average, but can have up to ~1000 transcripts. If this is correct, in...

> @tnguyengel I noticed that VEP allows you to export annotations as a [JSON file](https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#json), so as another way to approach the problem I wondered if you could use that...

> Dear tnguyengel, did you manage to run the 5000 samples? > We just released a new version (2.3.3) that aids with some issues and are improving on merging large...

Do you suggest merging different families or different populations in separate batches so that we can tweak the merge settings to be more aggressive within a family or within a...

I would like to bump this. Unzipping VCFs for large datasets is highly undesirable in terms of storage costs. Most bioinformatic tools are able to operate off of either compressed...

Also getting this error. Jasmine v1.1.5.