Edoardo Giacopuzzi

Just an update on this. After several tries, I was not able to merge the whole cohort (79530 samples) in a single run, after ~1 week of running time it...

Unfortunately, I cannot split by chromosomes, since this would generate more files than my inode quota on the system can allow. So I merged PASS calls across all genome for...

I will do some more tests to find the best approach for merging, but right now I'm satisfied with 3 chunks. I will now test if the output VCF obtained...

I've fixed the problem with redundant anchor names. Now execution using `--lint` completes with no errors!

Thanks for reporting this. Actually I've tested it with cellranger count/vdj v6.1.2 and 7.0.0, probably they changed the HTML report slightly compared to v6.1.1. I hope the parsing schema remains...

Hi @chris-rands . The module works fine, but I've made a few recent changes to make the file search pattern compatible also with older versions of CellRanger v6, and these...

Thanks for the suggestion. From your example it seems I can filter for a defined list of samples, but how can I apply the same to compute DP across all...

Thanks, I'll look around for other solutions then. If you consider implementing something similar in the future, I would suggest making it possible to define GT subsets directly into the...

The same is happening here. Any attempt to download a model using the python API in our HPC fails due to connection timeout. However, manual download from the browser in...

Thanks for the explanation. So you are using this file `iGenomes/2023.1/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed` from the iGenomes release, right? I'm fine with excluding additional contigs (like decoys, HLA, ALT, etc.), but also excluding...