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spark things are falling over when they encounter the new hg38 contig names that include `:` and `-`
We need to update hadoop bam to understand these since they are an unfortunate fact of life.
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[Annels NE, Callan MF, Tan L, Rickinson AB. Changing patterns of dominant TCR usage with maturation of an EBV-specific cytotoxic T cell response. J Immunol. 2000 Nov 1;165(9):4831-41.](https://www.ncb…
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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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## Bug Report
### Affected tool(s)
ValidateSamFile and possibly other Picard tools with the same dependencies
### Affected version(s)
- [x] Latest public release version 2.9.2
### Descripti…
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Hi Brad,
What's your vision on updating the hg38 reference fasta to include the latest patches? Lately, we've run into some alt coordinates that aren't included in the current available reference,…
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Ran the README example (with small edit as curly-braces are wrong currently)
Log lines:
```
INFO:root:netMHCpan -xls -xlsfile /tmp/netMHCpan_outputnbiuow68 -l 9 -f /tmp/peptideoog0vb52 -a HLA-A01:0…
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There are some uncaught errors resulting from trying to predict binding for peptides that are too short or empty, and we should handle those better.
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Hi,
I meet a new error when I used pvac-seq, I use :pvacseq run TUMOR.vcf test1 HLA-G*01:09,HLA-E*01:01,H2-IAb NetMHC PickPocket NNalign /home/xuexu/Documents/melanoma_project/neoantigene/IEDB/pv…
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Trying with @armish's setup (since mine didn't work; see https://github.com/hammerlab/biokepi/issues/418), I get some of these, which I believe are issues with OptiType itself:
```
### Kube-Job 5a…
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We solved issue #285 by putting PR, RT and INT all on the HIV-pol seed. However, we still see some coverage drop offs at the edges of other HIV regions. For example, sample 44841AD4-HLA-B-E9253012800p…