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I'm getting this error when trying to run vt genotype
```
[parlar@mps 12191-96]$ vt genotype -r /home/bcbio_root/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -s 12191-96 -b 12191-96-ready.bam -o 121…
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Dear Freebayes Developers,
I am asking for your advice on a set of in/del variants that Freebayes seems to miss. When running FB 1.3.8 in debugging mode with -dd switch, one can see that these vari…
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This isn't supported in Zarr yet but because it is in Dask and the majority of genotyping data sets have major alleles with high frequency, there may be some significant speedups resulting from a spar…
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### Description of the bug
Joint germline genotyping completes actual genotyping, but fails at TSV count vcftools step
### Command used and terminal output
Command:
nextflow run nf-core/…
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Hi, I am using VCFtools - 0.1.16.
I subset a vcf file with vcflib, followed by bgzip and indexing with bcftools. (bgzip subset.vcf bcftools index subset.vcf.gz)
Then I used the following code for es…
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The function `sgkit.window_by_position` fails if the input dataset has contigs that lack variant sites, throwing an `IndexError`.
Traceback
```python
IndexError …
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It would be nice to have the ability to filter variants based on the alternate allele frequency in specific subsets of individuals. Currently, we can filter based on the counts of specific genotypes, …
arq5x updated
8 years ago
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Currently, `AlphaSimR::genParam()` returns genic variance that is in one way "realised" with respect to genotype freq and allele sub effect, but also "expected" with respect to mating, which is confus…
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Hi, I am trying to run GEM analysis, but it keeps showing an error about phenotype file. I have attached my code here. Do you know what is my problem here?
singularity exec \
> -B /humgen/ManningL…
lc491 updated
6 months ago
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## [Viral data.ipynb](https://github.com/maousi/HBV/blob/master/Viral%20data.ipynb)
You are looking at [NA values](http://localhost:8888/notebooks/Viral%20data.ipynb#NA-values). Plot 54 is great. I…