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Hi Carl,
I have some datasets with > 5 Million SNPs (but < 500 samples and 1 phenotype). The run with single_snp takes more then 8 hours. Is there any way to speed up things?
Thanks
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Hi,
I have a question regarding to how to prepare the snp by cell matrics, in your example, genotype vcf files are generated from single cells, where the ref/alt matrics could be told as I assume. …
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I have successfully run glmm.score, but am getting the following error with glmm.wald (using gds):
Error in if (is.gds) { : the condition has length > 1
R version 4.4.1 (2024-06-14) -- "Race for Y…
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I tried to retest the pipeline today and now am getting errors involving the automounter (autofs). I made no adjust for the automounter last week, but it seems to be an issue now.
Even when I atte…
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Hi,
We are looking to optimize the polishing step for reconstructing a plant genome using PacBio HiFi reads (Q30). Specifically, we tested both NextPolish and NextPolish2, followed by a variant cal…
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The latest version of trident has added a validation that the `NrSNPs` column is a value above 0.
While I agree that check makes a lot of sense, this requirement is not present in the janno_columns…
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Hi,
I'm trying to used fine-mapped results of complex traits from SuSiE as the input of fastENLOC as you recommended. I notice the following code you provided in input.md to help contrust the input…
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Download reads from [Sequence Read Archive (SRA)](https://www.ncbi.nlm.nih.gov/sra) for an organism with a good reference. If that has a high SNP count then it is a pipeline issue.
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Hi:
I used custom annotation information to generate matrix and tagging file using the LDAK-Thin model, and used LDAK-Thin to generate Per-predictor heritabilities. However, when I calculated the eff…
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When I specified the `--certs` option with `launch-qemu.sh`, it failed with the message: `Invalid parameter: certs-path'.`
```
$ sudo ./launch-qemu.sh -hda "../ubuntu1.qcow2" -sev-snp -certs /opt/…