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I am running RNA-seq pipeline on 12 rat samples. It seems GATK failed in the variant calling. The error information is as below:
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> 03:22:50.041 INFO GenomicsDBImport - Initializing engine
> 0…
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Hi!
Is it possible to detect mosaic events with strelka2?
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PHI base would like to be able to specify (in some cases), the methodology of the allele creation, as it can affect the expression level
The example provided was "promoter knockdown" vs. RNAi.…
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@LeeTL1220 commented on [Mon May 23 2016](https://github.com/broadinstitute/gatk-protected/issues/524)
- [ ] File issues for evaluations (and make sure each evaluation is described, including ground …
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will this package work in Mac OS?
I have tried installing... But no files getting produced in bin folder
```
make -f geneVarAssoc.mak OURFLAGS=-g
if [ ! -e ../obj ] ; then mkdir ../obj ; fi ; \…
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Hi,
thanks for a nice looking program. I'd be keen to try out the approach on F1 hybrids, but the documentation is not complete for this. Do you have any hints ?
So far I have created diploid pseudo…
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Hello,
After upgrading to the latest development version, the logs and joint VCF file generation don't seem to work properly anymore. Debug messages don't get printed anymore (neither on stdout, no…
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question from kim
For evidence filtering, should the drop-down just have all possible evidence types (with those with no annotations greyed out)? Or should it just have the ones that are actually i…
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Inputs:
- Transcriptome GTF file
- somatic VCF (SNVs)
- germline VCF (SNPs). This could be germline calls from the individual or simply a dbSNP VCF. To be this flexible we need to actually check for …
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Hi,
For an allele specific expression analysis, one of the ways to reduce ambiguous mapping reads is to extract or use only unique mapping (not referring to primary alignment or unique alignment here…