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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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Hi,
I have observed that some variants located at the ends of chromosomes seem to be unsuccessful in genotyping from all samples in my dataset. If this phenomenon is normal? Could you please provide…
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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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Dear all,
I read the paper which is involved MarVin, but I have a question only just to clarify me...
MVN call in 1000 Genomes or GoNL was used in order to phase large SV, it not sense the type …
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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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Hi, What would be the best way to select k with ohana results?
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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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I have an example where we miss a very clear resistant call due to LOW_GT but the depth on alt vs ref is very obvious. I appreciate it is hard when we are drawing lines based on percentiles. Anyway, I…
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Did you changed the way you are using for calculating distance matrix. I want to understand your code. I the first version you were calculating the jointclass matrix for shared alleles and then you ar…
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Hello I am using bcftools to call variants with this command:
bcftools mpileup -B -q30 -Q30 -f reference.fasta -a FORMAT/DP,FORMAT/AD --threads 6 -R list_of_specific_position.txt file.bam | bcftool…