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On recent 1000 genomes data, we have the following:
```
39G 20201028_CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.recalibrated_variants.vcf.gz
```
The zarr using defaults is:
```
43G tmp/1kg_ch…
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### Installation Type
Standalone
### pVACtools Version / Docker Image
3.1.1
### Python Version
_No response_
### Operating System
_No response_
### Describe the bug
hello,
With ref-transcrip…
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Some variants are described in terms of exculsionary criteria. These will need to be considered in our model.
See https://civicdb.org/events/genes/5/summary/variants/2408/summary#variant for an exa…
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Hi - thanks for making these data and code available. I have installed PRSice and cloned the repository, Using the code snippet that you posted here, I tried to run PRSice. Howver, it seems the summar…
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Per CPIC SOP guidelines, the HLA phenotype is expected to be classified as either positive or negative. Nevertheless, our reports indicate that the phenotype is sometimes recorded as n/a (not applicab…
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Dear pairtree team, and Dr. @ethanumn.
I really appreciate this wonderful program.
However, I have several questions.
Q1.
In the output of pairtree, the number of node has one more cluster…
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The MAC codes that have allele field expansion should only work with the same antigen field as that in the MAC.
`DRB1*07:DFJR` expands to `DRB1*15...`, `DFJR` for DRB1 should only be valid for `DRB…
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Hello, I'm trying to get the pipeline up and running with the example dataset, but I keep getting this error that are no alignments in the bowtie log. Because of this error it doesn't produce the Clas…
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Hello,
I successfully ran countLociImmanc.sh on both my data and the example data (spd_ARU+182+BOU.str.immanc), resulting in 28816 and 307 loci, respectively. I noticed the code in the readme spec…
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Working to reproduce `example.sh`. I've gotten part way but seem to be running into some kind of server error. I've made some minor modifications along the way to allow `example.sh` to be run without …