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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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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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Hello! I am interested in learning more about this parameter:
```--pairwise_del: pairwise deletion of missing data.```
I have noticed that using it has a very large influence on my results, but I ca…
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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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Currently, figuring out what fields are available requires running a command like:
```
gsutil cat gs://gnomad-public/release/2.0.2/vcf/exomes/gnomad.exomes.r2.0.2.sites.vcf.bgz | gunzip -c - | head …
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Hi,
I wonder how the genotypes of the parents are corrected using the progeny allele counts. I guess with "correct_variant_types()", in offspringscoring.py? What I find strange is that on my VCFs s…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/107) by Tobias Marschall (Bitbucket: [tobiasmarschall](https://bitbucket.org/tobiasmarschall), GitHub: [tobiasmarschall](https://githu…
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```##ALT=##INFO=```
```##FORMAT=##FORMAT=```
Missing newline
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Hi, I obtain a `.pop_like.txt` with all nan values after assignment and couldn't figure out what would be the problem.
I use a reference (breeding) population: 60 individuals from 12 populations 4…