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The HM2 pipeline phasing firstly and run scaffolding software on the reference haplotype.
If you have two contigs of different phases, the scaffolding might join these two contigs together and introd…
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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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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/14) by me.**
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GATK outputs a PQ tag for each phased variant (except the first). We should do…
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Copying a comment from a discussion here
https://github.com/Mu2e/Offline/pull/379#issuecomment-803443585
I think StepPointMC is a bit of a mess because it is trying to cover too many use cases.
I…
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# Background
We added `use_modular_headers!` to our `Podfile`s as we originally planned to phase out `use_frameworks!` (see https://github.com/flutter/flutter/pull/42204). However, our plans have n…
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Hi,
Trying to do some compartments on a bacterial chromosome (fasta file with only one sequence), I got the following error message. If I am not doing the phasing, the function works.
```R
lib…
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Hi,
What is the best option to phase the assembly, parental data or Hi-C, or both? For a specific case, I have both data available.
Cheers
André
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### Current Behaviour
Currently only tested in the worgen area. Quest Royal orders when clicked auto accepts the quest and gives you no additional quest text and no way to close it other than using e…
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Hi,
This is just a question and not an "issue"... I was wondering if if Bigdawg is able to do phasing for subsequent imputation using other programs.
I noticed in the 2016 Human Immunology pape…
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(Not released)
Occasionally fall through a wall.
Walk up to a steep part and kinda jump along it. You'll find a spot and fall through