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Hi, i'm testing GAUDI running it to more than two ancestry. To check this before using real data, I changed the msp files from the toy data manually, changing some numbers 0 and 1 to 2 or 3. I am not …
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I have found a rather amusing edge case in the haplotype trimming code where by dumb unluck we we threw away all the haplotypes in an assembly region. At this site we have discovered variants from the…
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**1. What were you trying to do?**
Haplotype sampling
First step is preprocessing the graph
**2. What did you want to happen?**
Successfully generate `sample.hapl` file
**3. What ac…
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Hi developers of `longphase`,
Recently I use `longphase` to phase the ONT sequenced patient data. The phased result looks good but I want to convert the phased VCF to two seperate fasta (one for m…
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How to combine the Shapeit4 phased variants across different chromosomes? Could I run Shapeit on all chromosomes together? I'm using a pedigree-based phased vcf as scaffold. The paternal/maternal assi…
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Following [Kaput _et_ al. 2014](http://onlinelibrary.wiley.com/wol1/doi/10.1111/mec.12594/full), implement the haplotype calling algorithm based on the binomial confidence interval.
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@usolloch @sauter
Thank you very much for developing this software, which is very helpful for HLA calculation.
I have some questions about the calculation results, and I hope you can give me some …
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There is a section in "tools" in which a `compute_pairwise_coalescence_times.py` script is used to calculate pairwise coalescent rates between one haplotype and the others. But there is no file called…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Cercis/canadensis/genomes/ISC453364.gnm3.GWXB
- Cercis/canadensis/annotations/IS…
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Hi,
We've been trying out rpvg on a crop plant and it looks very promising!
I have a question regarding inferring haplotype probability when read counts are 0.
Index was built using autoindex and q…