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The **'Case-Control' Annotation Type** we proposed a Variant Annotation category in our initial list [here](https://docs.google.com/document/d/1csUrC4kX6G1V1GIz07btQQ3oL_cdDPJShuauL_uCjEw/edit#headin…
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I am using Deepvariant to obtain vcf files for single individuals and merge these files with GLnexus. I am having 2 issues.
1) I observed that a 0/0 is coded if an individual is homozygous referenc…
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In James B's article (https://doi.org/10.1093/sysbio/syv023), it is mentioned that:
> The f-statistics (f4 for a four-population clade) are analogous to the D-statistic in form, but use population …
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It would be nice if the data in the network (edge list, rates, allele frequencies) could be obtained as useful R objects.
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The workflow could be run on all amplicons only (and not specific target SNPs aswell). If we can reduce the number of inputs for some users that's a bonus.
Things like allele frequencies and cover…
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@gregorgorjanc @RosCraddock
Originally, while estimating the alternative allele frequency of the whole population, the algorithm looped over the genotypes of all the individuals to calculate the most…
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The Bravo variant browser currently shows chromosome locations, alleles, VEP functional annotations, and allele frequencies for 463 million variants observed in 62,784 individuals sequenced in NHLBI's…
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With #356, the VCF file created by `intrahost.py`'s `merge_to_vcf` reports read depth, at a given position, only for samples that contain alternate alleles at that position. If a sample has no alterna…
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Would it be possible to allow the program to take numpy files as input (eg, allele frequencies from pcangsd)? I get a segmentation fault when I try to use the npy file from pcangsd, but it runs when I…
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There are hard treshholds in the scripts that filters false positive somatic SNVs/indels. These pertain to the read depth, allele counts and fraction as well as gnomAD population frequencies and PoN c…