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In allele frequencies, vgsc diplotypes, and ancestry
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For discussion:
# Specification: VCF to VRS Processing Package with Cohort Allele Frequency Generation
## Overview
This package processes Variant Call Format (VCF) files to ensure compatibility…
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Hi developers,
While performing GWAS using fastGWA within GCTA on our pgen genetic data, some snps are removed (1960 out of 16084709, with sample size=9217). While forcing GCTA not to filter them u…
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Hi,
in the first place thank you for the effort you made with Strelka and for how well it is documented. I know from [here](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#…
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Hello,
I successfully ran est_p, and am now trying to estimate the hybrid index using default settings. The data for the putative hybrids is formatted the same way as the parentals, but I am gettin…
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Hello,
I've been using your Revelio with Freebayes to call variants on methylation libraries. We were able to get good agreement between our methylated libraries and benchmarking variant dataset. …
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Extract heterozygous allele frequencies from the tumor sample VCF, and segment those values to generate a .cns file. CBS, haar wavelet and fused lasso are all fine algorithms for this.
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Hello,
My group member and I are interested in the HEGP challenge. But we cannot find the allele frequencies of the plaintext that you mentioned on the website. That will help in defining expected …
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Dear Manny,
I am trying to have access to an old raster.RData that was used as for plotting allele frequencies in world map:
`load(url("http://github.com/mgimond/Spatial/raw/master/Data/raster.R…
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Currently we support `t_alt_count` and `t_ref_count` (and `n_alt_count`/`n_ref_count`) in the MAF and calculate allele frequencies based on these columns. But often time, we only have allele frequenci…
jjgao updated
3 years ago