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I'm trying vcf-tools for the first time. I cloned it here from git, and installed it using...
EPREFIX="/tmp/vcftools/"
PREFIX="/tmp/vcftools/"
DATAROOTDIR="${PREFIX}/share"
DOCDI…
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@arahuja implied there had been some discussion around this in the past.
AFAICT there is no good way right now to capture there being two non-reference alleles at one locus, having [one `Variant` per…
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`dng call` gets `Segmentation fault (core dumped)` when PL is used.
- Implement warning/debugging message.
```
##FORMAT=
```
Thanks @cryancampbell
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...
Removing 259 variants outside intervals.
INFO [2018-02-25 11:14:01] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
Error: logical subscript contains NA…
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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:
>
> 03:22:50.041 INFO GenomicsDBImport - Initializing engine
> 0…
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If we have overlapping read pairs, overlapping bases are being double-counted in the genotype's "DP" (depth) calculation, and possibly when genotyping. Prior to HipSTR, we can certainly use tools lik…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/139) by Justin Zook (Bitbucket: [jzook](https://bitbucket.org/jzook), GitHub: [jzook](https://github.com/jzook)).**
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@ldgauthier commented on [Wed Oct 21 2015](https://github.com/broadinstitute/gsa-unstable/issues/1185)
@vruano and I both looked at this and we can't figure out why this globalPrior (by default 0.001…
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Genotype Phred Likelihoods aren't restricted to
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If saving a blocked gVCF where the non-reference blocks do not have likelihoods attached, we get the following error:
```
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
at htsjdk.variant…