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Per the README, and sounds like @rleonid has always done this:
> Optional step zero: you might want to filter your sequencing data for HLA reads. Should you have to re-run OptiType multiple times o…
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I have a 28GB bam file, and I'm running into memory issues with Razers3 even when I allocate 32GB of RAM for this job. Do you have any recommendations on what to do? Thanks.
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I’ve used the cnvkit a few times, but this particular sample results in stating everything is at a loss.
This is the head T1.cns file produced by bcbio (i removed the gene column for clarity)
``…
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Hello,
I am trying to install bcbio on Temasek Life science HPC in Singapore and got the below error,
The following packages will be DOWNGRADED due to dependency conflicts:
fontconfig: …
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I'm very new to linux and installs such as this, sorry if this is a silly question, I do feel like I'm missing something obvious. I keep getting a conda lock error. I've tried installing multiple time…
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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=…