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The mapping VCF genotype values to GA4GH `Call` objects is currently incomplete/incorrect. Questions:
1. If the delimiter is `|` then the genotype is phased. What should the value of the `phaseset` f…
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GATK uses AD=ref,alt1,alt2...
freebayes uses RO=ref, AO=alt1,alt2
it would be nice if these were pulled when doing the decompose (and then used to recalc DP) so that they could be used downstream to …
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As part of our removal of wormtable detailed in #210, we need a performance comparison between the HtslibVariantSet and the WormtableVariantSet. This should use the `server_benchmark.py` script.
Befo…
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Hi Brad,
I am using version 0.1.9 standalone jar of bcbio.variation. I am also running java version "1.7.0_60"
When I run bcbio.variation ensemble on 3 vcf files (GATK-UG, HC, Freebayes) I continuousl…
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Even though this same error has been reported and closed in #675, I am now experiencing it with a fresh (isolated) install/upgrade on 12/31/2014 for the "exome with validation" pipeline at http://bcbi…
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The variant-ensemble command is failing when called from the bcbio-nextgen "ensemble" stage for the "Exome with Validation Against Reference Materials" example pipeline (yes, I've had horrible luck ge…
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bedtools intersect gives me different results when using vcf files instead of bed files (which are identical). Why is that or is this a bug?
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Seems to be the ensemble calling?
java.util.ArrayList cannot be cast to java.lang.String
Sending the entire output:
> parlar@v01s979:~/projects2/testbcb/140819-M00568-0081-000000000-A70K0/calling/…
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I posted this to the mailing list since it might end up being more of a "I just don't get it" issue instead of a problem with the code (or docs).
https://groups.google.com/forum/#!topic/freebayes/fZIj…
travc updated
9 years ago
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I run isaac_aligner followed by isaac_variantcaller on four different synthetic datasets of WGS
at 50X coverage and different error rates: 0.1 0.01 0.04 0.05
paired reads, 100bp read length.
For eac…