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Hi Devon,
Thanks for this really helpful tool!
I noticed that the "assess_missing_data" functions will throw an error if the VCF file has phased genotypes (i.e., the delimiter is a "|" instead o…
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We currently have a folder called `delete_me` in the modules repo.
This contains a wide range of files that have been deposited, mostly for specific modules.
It is NOT included in the README file, …
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Hey all,
I would like to use G2P software for my population genetics analysis. I converted the dbSNP VCF file into a ped and map file but when I start a single population simulation I get no result…
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I keep getting just "0" or "1" for genotype after ~560,000 correct conversions using the 23andme_v4_hg19_ref.txt.gz data and after ~500,000 correct conversions using the 23andme_v4_hg19_ref.txt.gz dat…
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Some points to consider in get_genotype_vcf.py
- [Extracting the chr values from the bim](https://github.com/populationgenomics/saige-tenk10k/blob/4f00b431e873f98f7c3890ebdb191fb80d975568/get_genot…
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HiFiCNV currently outputs `0/1` as a placeholder GT value for all cases. Set policy to either make this unknown or provide a consistent interpretation of copy number as GT.
ctsa updated
7 months ago
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Many strains do not have a genotype, either because it was very difficult or nobody in the long history bothered. Here are some solutions to deal with some groups of strains automatically. After that,…
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A typical genotype entry looks like:
`0/0:43,0:43:92:0,92,1267`
The first part `0/0` is the actual genotype; the others are genotype annotations. In our current implementation (vat 2.0 hereafter…
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Working with a large-ish dataset (30TB raw reads), and was wondering what a good strategy would be for working with the joint_germline option to get cohort SNP calls. Would it make more sense to try …
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We're trying to use SNParcher on some fairly large genomic datasets at the moment (2000 + individuals), and I am anticipating a lot of slow-down at genotyping steps. I was wondering if it's possible t…