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Hi, thank you so much for the great tool!
I was wondering whether we could obtain read-level phasing result for the input bam. I checked the test_pipeline output but I think we only have isoform-le…
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Thank you very much for creating amazing resources!
Quick question: do you plan to release phased chromosome X any time soon?
Thanks again!
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The covariance calculation should be weighted by the magnitude of the data -- currently all points in the complex plane are weighted equally, but the ones with more magnitude (further out) are more im…
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Coming out of #2403:
> For 2, the final HM will have the addition of both horizontal lines separating phases, and the ability to move loci up and down to be in the right phase if they are not put th…
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A small discussion happened on the Slack #project-modsecurity from OWASP where I pointed out that, with TW changing ownership to OWASP of modsecurity, the domain name might need to be transmitted so t…
vloup updated
1 month ago
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Hi, I'm excited to use this tool to evaluate my imputation results. But I bump into this error with my test cases even though I have run successfully with the repo's test set.
This is my R script:
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Hi,
I am trying to phase 21 individuals with shapeit5 but I get the error "Less than 50 samples is not enough to get reliable phasing, consider using a reference panel to increase sample size". I …
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It'll frequently be the case that singletons are not phased. Singleton variants aren't used by tsinfer, but are crucial for correct dating. Here's how we'll handle unphased singletons:
1. Split edg…
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The [VCF 4.4 spec](https://samtools.github.io/hts-specs/VCFv4.4.pdf) allows for an initial symbol indicating the phasing of the first allele. For example, `/0/1` is a valid genotype. This allows for p…
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I understand that it has not been published, and I do not know if it has been benchmarked in any way. But in theory Pangenie offers variant phasing via an hmm-based algorithm, which seems sensible.
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