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I'm using this sequence (A*29:02:01:01 with truncated 5' and 3' UTR sequences that include two 5' and one 3' UTR changes) to test the act operations:
`cgcgtggctctcagagtctcaggccccgaaggcggtgtatggattg…
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I ran tumor variant calling using an ensemble caller with vep annotation + hla calling for normal. I successfully obtained an annotated ensemble vcf, but the expected .csv containing optitype output …
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I was wondering if there are any plans to support GRCh38 as an additional assembly. The alternate loci and decoy sequences are likely to improve both variant calling and expression studies. I suppose …
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Hi,
I wanted to understand better the 1st step of HLA typing using Optitype in bcbio i.e. aligning to hg38 to extract fastq reads in HLA regions.
Are you using bwa-mem to align to the reference fast…
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Hello,
I'm getting the following error during a germline variant calling analysis: "sambamba-view: not enough data in stream"
These are the last lines from bcbio-nextgen.log:
> [2017-06-22T22…
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it may be a good addition
http://www.bcgsc.ca/platform/bioinfo/software/hlaminer
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Hi Brad,
I am working through the tumor/normal synthetic 3 Teaching example for bcbio-nextgen, but I am receiving an error from the OptiType HLA typing:
```
subprocess.CalledProcessError:` Comm…
ghost updated
7 years ago
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Hi,
I am currently running the HLA typing software portion of the MHC-PRG package. I set up the commands as described in the github descriptions however when I ran the program, I received this error:…
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Hi Brad,
I found one sample in my batch stuck during the freebayes variant calling in the cancer somatic variant calling pipeline. I deleted this sample in the yaml file, the remaining pairs all fini…
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```
./cocosubmit.native: internal error, uncaught exception:
Nonstd.Option.No_value("Can't find metadata: \"Seq2HLA\"")
Raised at file "bytes.ml", line 2…