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Hi,
I am running into an issue with the HLA typing that I cannot figure out. The program fails with the message:
Traceback (most recent call last):
File "bin/optitype_ext.py", line 31, in
…
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https://github.com/genome/docker-immuno_tools-cwl/blob/ef53b1e390a52280b362cd8a62237cd210ff4b71/Dockerfile#L1
The purpose of this container is only to add tools and configuration settings needed to…
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Hi~ Thank you for this wonderful work, i would like to know about an issue i came across.
KIR3DL3, KIR3DP1, KIR2DL4, and KIR3DL2 are four frame kir genes which in principle every individual should h…
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Hello!
I'm trying to run the docker image via singularity bootstrap, since the HPC does not provide root access for docker. What would the command equivalent for -v, -t, and -i, -o in the Docker comm…
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Hi,
I am trying to use conda release
conda install optitype
by using
https://bioconda.github.io/recipes/optitype/README.html
You may consider adding this option to GitHub README
Thanks…
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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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Hello,
I installed optitype using the following command:
conda install -c bioconda optitype
No errors were reported. but it seems that the machine doesnt recognize the pacakge:
I executed:
…
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Hello,
I tried to run Optitype with a BAM produced with BWA-mem.
I ran into the following error:
File "/usr/local/bin/OptiType/OptiTypePipeline.py", line 358, in
pos, read_details = ht.pysam…
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Hi,
OptiType has been reported as one of the best performing tool for genotyping HLA Class I alleles, but unfortunately, OptiType does not type HLA Class II alleles, which may limit its clinical util…
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https://github.com/namphuon/ViFi
Docker image and Dockerfile is there.
I think this tool makes more sense than GENE-IS; we're investigating if there are differences.