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Please place an "x" in all the boxes that apply
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- [x] I have the most recent version of poppr and R
- [x] I have found a bug
- [x] I have searc…
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## The problem
Parsing the same VCF files repeatedly is a serious bottleneck when working with TOPmed data (54000 human samples over 480 million variants). The following numbers are for chr17. Mult…
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Hi,
I came across some unexpected behaviour whilst running a recent analysis. In my analysis, I'm using vcfR's is.polymorphic() command to tell me which SNPs in two population-subsampled VCFs are p…
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Hi,
I may have encountered some pb during a re-genotyping process, failing to get the original input alleles;
sorry by advance if this is not relevant;
In a somatic calling diagnosis context,…
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Hi everyone,
I have recently tried to calculate admixture proportions of a large number of individuals (of several populations) with fastNGSadmix, when compared to a reference panel with two popula…
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At a minimum, we need to be able to calculate these axis-wise aggregations (for GWAS QC):
- [x] Variants (across samples)
- [x] genotype counts
- [x] allele counts and frequency
- [x] call…
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## Describe the issue
Error when running filter_vep,
File "input file" does not look like a binary file
## Additional information
Please fill in the following sections to help us find the source…
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Hi
I'm using bcftools: Version: 1.9-290-gb224270 (using htslib 1.9-456-gc1c8c80)
I'm wondering why after annotation, it seems like the second allele (**CCCAG**) is deleted from ALT column in the…