Comments (3)
It should still run through, it was just an unescaped percentage sign in a string substitution one line above, fixed now. BTW, why do you have so many unpairable reads? Could you run this with deletebam=false in the config file and e-mail me the intermediate bam files and the coverage plot? I've never come across a sample like this (which is the reason that unescaped % went unnoticed for so long :))
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And forgot to answer your question: you get this warning if your HLA reads' individual ends can't be paired up consistently (i.e. both ends mapping to at least one common allele) for more than 10% of them. I could only see this happen for very long insert sizes where one end always falls in the exon2-exon3 reference window but the other is always left out.
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hi @andras86, I fixed the unescaped % and found a bug in my code. The pre-filtering step was not done correctly and generated a lot of unpaired reads. Btw, I ran Optitype on a whole bunch of samples and you might be interested. Let's take this offline. Thanks for your help!
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Related Issues (20)
- The SolverFactory was unable to create the solver "glpk" HOT 1
- OptiType returns ValueError with some samples while running just fine with others
- could not open alignment file HOT 4
- output file column description
- error using docker
- Hi dear @andras86 , What's the meanning for "introns from " as picture beblow? I found it apprearing in https://github.com/FRED-2/OptiType/blob/master/hlatyper.py HOT 1
- Does OptiType only predict alleles in "freq_alleles" HOT 1
- Is it based on hg38 genome? HOT 3
- ValueError: too many values to unpack
- Maximal read length of 0 bps exceeded
- Want to use Optitype HLA results as input file for pVACseq, if someone could provide suggestion? HOT 2
- Installation problem with pyomo module HOT 1
- this team is no longer maintained HOT 1
- HLA typing 10x scRNA-seq data with Optitype
- unpaired reads, no mismatches, ambiguous HOT 1
- Razers3 being slow HOT 1
- Issue with downloading OptiType docker image HOT 1
- core dumped bad_alloc in seqan HOT 6
- Bam file to prefilter reads HOT 1
- IOError: [Errno 2] could not open alignment file
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