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Dear OptiType,
May I ask does Optitype support MICA, MICB typing? It work pretty well on genotyping HLA genes, but will it also work on MICA and MICB? Thanks in advance.
Yours,
Ying
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### Description of feature
Hello,
As described in #145, adding more typing tools could allow us (among other things) to set up a result combination algorithm. If you compare it to other, `HLAsca…
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The 4th field of HLA nomenclature includes:
1. intron variants
2. UTR variants
Due to complexities in the typing of UTRs and also/especially the dynamic nature of their definition in the IMGT/HLA…
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here is the full output:
```bash
[12/Jun/2020 16:16:54] INFO - Xie Chao's HLA typing algorithm
[12/Jun/2020 16:16:54] INFO - Sample_id: 09KTG_TGACCA Input file: ./results/mapped_reads/09KTG_TGACC…
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I am able to perform the 4 digit typing on the sample data (test.bam) using the following command line:
docker run -v `pwd`:`pwd` -w `pwd` humanlongevity/hla \
--sample_id test --input_bam_pat…
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Hi
Can you explain how you calculate CDS distance, CDS consensus and CDS mutations?
Thanks
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Dear Sirs,
I am trying to make HLA Genotyping for HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB2 and HLA-DQA1. Please tell me where can I find the HLA reference files in VCF format, as it is required for …
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run command:
hisatgenotype --base hla --threads 4 --bamfile SRRxxxxxx.bam
BAM file is generated previously by STAR 2.7.0
--------------------Python error trace message:
Traceback (most recent cal…
nikyk updated
2 years ago
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Hi hista-genotype folks,
Our group is very interested in your software to determine the haplotypes of patient samples.
We sequenced the HLA-A and HLA-B loci.
When we run your software it typical…
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Great idea to make this a separate tool, I've found a need for MHC parsing outside of prediction as well.
For class II alleles with alpha/beta chains, NetMHC requires them to be entered as paired all…