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I want to perform a GWAS on a beagle file (with genotype likelihoods, which was generated from [`atlas`](https://bitbucket.org/wegmannlab/atlas/wiki/Home)) for a low-coverage WGS project.
`angsd -…
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Hi~
In the last days, I tried to use kage to genotype my population, but it won't work well, please help me take a look:
'''
kage genotype -i 2/PN2_SNP -r data_tmp/CRR493563 -t 16 --average-cov…
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I'm running GLIMPSE2_phase v2.0.0 which is up to date for 1 sample for chromosome 1.
Here is my script:
```bash
GLIMPSE2_phase --input-gl /data/GL_file_merged/high_dep_100.chr1.vcf.gz --reference …
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The VCF file format appears to be a popular, powerful and (comparatively) well specified file format for genotype data. Poseidon could (one day!) support it the same way it supports Packed PLINK and E…
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At some positions (such as 20:10001430 in src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf) reads with mismatches or indels in the BWA-aligned p…
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Hi, Dr. Josh.
Recently, i am focus on calling SNPs in a polyploid species.After manually check the original code, i found there may be a bug in the "Haplotype.py" script. The possible mistake …
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Raising this issue to discuss implementing a function to convert a [genotype call array](https://discourse.smadstatgen.org/t/n-d-array-conventions-for-variation-data/16/4?u=alimanfoo) to a dosage arra…
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I suggest to add a new tag `aDNA kinship`. This is a topic with obvious relevance for archaeology. Papers about biological kinship are usually developed in close collaboration of geneticists and archa…
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Hi,
I have a question regarding gt_depths. On the website website "https://gemini.readthedocs.io/en/latest/content/database_schema.html#the-variant-impacts-table" it says, that gt_depths is "A comp…
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Hello,
I want to obtain heterozygosity values for my individual samples. I have a doubt regarding on how to account for HWE when doing this.
From what I have seen, the standard procedure is to …