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Dear Manny,
I am trying to have access to an old raster.RData that was used as for plotting allele frequencies in world map:
`load(url("http://github.com/mgimond/Spatial/raw/master/Data/raster.R…
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Hello, I would like to study the genetic correlations of several diseases in East Asians, and below is the log file. I am wondering why so many SNPs are being excluded due to valid alleles QC. Could y…
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I wonder if it would be better to make the arguments for the table header be mandatory.
The defaults (HOM_REF, ALT) are confusing and wrong
This is the header of a table that I adjusted manually a…
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### Description of the issue:
When reading a VCF with HTSJDK it causes an exception when there is a duplicate ALT allele.
I believe duplicate ALT alleles are allowed in VCF, and are used in cases wh…
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There are some studies cannot be harmonised, but they are labelled as pre-fwas-ssf or gwas-ssf. Need to resign the file type into 'not_harm".
- 3 studies PMID_37592023 - gene_based
- 594 studies PMID…
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Hi,
We have some tools that expect to see allele depths in FORMAT column (ie A,C,G,T or AU,CU,GU,TU) and TIR/TAR for indels. Would be great if there was a way to get these in the vcf output.
Tha…
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###########error##########
getAllelesForAA(HLA_AA,"DQB1_77")
Error: allele DQB1*02:180 could not be found in the alignment file
Execution halted
#######################
I expected that midasH…
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### Description of feature
allele_id and allele_name are currently written and extracted to/from text files containing the peptides. Adding the allele information to the meta map increases code reada…
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It should be possible to give each `Organism` a color or even a number based on a certain allele.
```
You toggled the view for the gene
```
We already have the gene names...
https://github…