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Hi,
It seems that for samples in which a variant was NOT detected in a cohort, that GenotypeGVCFs is putting read depth in the AD and DP FORMAT fields of those samples' gVCF MIN_DP fields, rather tha…
gevro updated
1 month ago
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Vcflib `vcfbreakmulti` doesn't handle annotations correctly during splitting
- [x] create megSAP test for this error (e.g. calling on the extracted region of DNA2106177 shown below)
- [x] test if Vcf…
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Dear @tobiasrausch,
Hi. I'm Oh.
I executed the delly for Germline CNV calling.
I want to ask about the genotype of my called CNVs (c1.cnv.bcf), or merge the calls (merged.bcf).
```
re…
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Currently, `mps-data.json` is a dictionary, mapping SNP reference IDs to a set of fields: [phenotype, pathogenic, gene, notes]
My understanding is that in reality, each SNP is a "folder", and the s…
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I have been trying to get hogwash v1.2.6 to run using R v4.1.2. However when I run hogwash on the example dataset I get the following error
```
phenotype
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I assume that if this is haploid data, we don't need a call_genotype_phased array to show that the data is phased? Unless the suggestion is that haploid data without a call_genotype_phased array could…
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i am facing this error while numericalization of hapmap file
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Hi, I ran the gapit script for 50minutes and showed the bug "Error in hist.default(r1, plot = FALSE) : invalid number of 'breaks' Calls:". The results show Kinship and PCA plots,but I thought the Kin…
lr192 updated
3 weeks ago
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I've just noticed something very odd while observing the resulting VCF file (the first one, containing both linked and unlinked SNPs). For a given locus containing multiple SNPs (i.e. more than one po…
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Hi,
I am a new user of the `coloc` package and need clarification on how to correctly set up input parameters, particularly `MAF`, `N`, and `sdY`. I am working with GWAS and eQTL data, where the GW…