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### Instructions
The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc. should…
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Hi,I am a user of scHLApers, thank you for developing such an excellent tool. Could you please explain how the files Sample_1006_1007_alleles.csv and Sample_1050_1051_alleles.csv on the GitHub web…
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Here's a quick way to reproduce:
```
# download GRCH38 and make sure there's no index
rm -f GRCh38_full_analysis_set_plus_decoy_hla.fa*
wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/…
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Hi again,
I have downloaded the Alignments_Rel_3330.zip from https://github.com/ANHIG/IMGTHLA and put the hla_nom_g.txt in that folder. It seem to be working fine at first to create the new referen…
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Using `netmhccons` results in these errors, which come from `netmhc-3.4`:
```
Traceback (most recent call last):
File "/Users/julia/code/netmhc-bundle/netMHC-3.4/netMHC.py", line 535, in
…
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Hi,
I am using BWA to map my FASTQ file to the hg38 genome. However, when I run the 'stats' command, it consistently stops at the beginning and throws the error message mentioned in the issue title.
…
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Hi Heng,
I'm trying to generate the hs38DH genome using the script in bwakit. If I use the data in the github repo, the necessary resources folder with the HLA and decoy sequence fasta isn't prese…
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Hello,
I constructed the graph pangenome according to the process (https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md (the quick start section)) you gave.
The first tw…
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I have installed HlaTools sucessfully. But I don't know how to construct config file and input file. Can you give me an example? Thank you very much!
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Objectives of the tool:
- Create a subdirectory to store the essential information (files) needed for review
- Create a Tiered and Annotated report table that makes it more clear which fusion cand…