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HaplotypeCaller is ignorant of read pairs, which is sad, because we're throwing away valuable information. Here's what needs to happen to fully utilize pairs:
- [ ] Make sure downsampling removes bo…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/192) by Michael Wykes (Bitbucket: [m_wykes](https://bitbucket.org/m_wykes), ).**
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Would it b…
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Walk finds ptsI-1 with`"min_non_zero_depth": 4, and "median_depth": 26,`
The reported sequence mapps to ptsI-1 when mapped against the reference panel with bwa mem.
DNA_sequence_identity 92% & Protein…
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Hi,
It is mentioned in the Denovogear paper that the software implements Denovogear (using SAMTools genotype likelihoods) and DenovogearBB (beta binomial based likelihoods). Actually, I'd like to…
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Hi,
Thanks for developing such an interesting tool, that could make the difference in the application of conservation genetics ! I wish I will be available to run feems on my dataset.
Could you pl…
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```##ALT=##INFO=```
```##FORMAT=##FORMAT=```
Missing newline
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Freebayes outputs VCFs with genotype likelihoods of format GL (which are not phred scaled) instead of PL, but I found that demuxlet failed to produce reasonable results using those as the field input.…
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The probe generator is making one probe for each 1bp and 2bp deletions in katG and pncA. But if you make a all 1bp deletions in a homopolymer, they are essentially the same.
eg deleting one A from AA…
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I've run Manta on a WGS sample and one of the called variants was labelled as "HomRef" in the FT field in one sample:
> chr1 2789490 MantaBND:0:14411:14412:0:7:0:0 T ]chr11:44096312]T …
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Hi,
I have a question about MNP handling in 1.0.9.
I created the following minmal test VCF:
```
##fileformat=VCFv4.2
##fileDate=20231214
##source=freeBayes v1.3.6
##reference=/tmp/local_ngs…