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it may be a good addition
http://www.bcgsc.ca/platform/bioinfo/software/hlaminer
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Hi there:
I'm interested in using the OptiType HLA genotyper with RNA-Seq data. I've done this using the stand-alone OptiType tool with good results so far, but I'd like to try scaling it up within…
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Would you consider a patch adding Python 3 support to OptiType? This would greatly simplify our lives at the place I work as this would make OptiType integrate better with the rest of our stack.
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Hello,
I'm running an analysis where some of the regions are HLA regions that have multiple haplotypes of chr6. The reference used is hg19.
Unfortunately, in these regions I get an alignment with MQ=…
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We'd like to experiment with OptiType and I'd like to fix on a particular code set. Instead of relying on a commit, would it be possible to have a tagged version?
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Hi Brad, I have tried to update my bcbio with bcbio_nextgen.py upgrade -u development --tools --data and But I receive.
I guess the problem is with age-metas dependencies.
Thanks!
Unsatisfiab…
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Hello all,
I was wondering how OptiType handles ambiguous results. I would expect that the solver returns something along the lines of "no single best solution found" or similar. Or will all best res…
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Thank you so much for pushing the fix for the segfault! When trying to update using bcbio-nextgen.py upgrade --tools, I got this fatal error:
Traceback (most recent call last):
File "/share/PI/eua…
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unable to install on m4.4XL instance
"sudo python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local --genomes GRCh37 --aligners bwa" aborts see below:
Please consider posting the…
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Hi,
When running against the test data, I'm getting the below error that I think traces back to GLPK but I'm not sure. Can someone help me possibly debug this issue?
**Here's the shelll script I use…
ghost updated
8 years ago