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This is what we discussed at the meeting today. I am just documenting on github issues for future reference.
 population: 60 individuals from 12 populations 4…
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Here is an example variant, http://brcaexchange-dev.gi.ucsc.edu:9003/variant/242491 a.k.a. chr17:g.43115727:T>G. This variant has allele frequency data from gnomAD but no other repo, and its allele f…
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[VariantContextUtils](https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java) currently calculates allele frequencies using AC/AN, but thes…
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Hi,
I'm looking at the MTAG output file (tutorial_results_1.1NS_trait_1.txt) and I'm wondering how allele frequencies are estimated (rs2736372 , freq = 0.4179).
I suspect that MTAG reports the …
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A suggestion for allele frequency calculation:
``` julia
### freq - calculate allele frequencies
# allele = 0, 2 for missing or heterozygous genotype frequencies
# 1, 3 for allele A, B incl…
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Can you clarify what "incompatible allele" means versus ambiguous, palindromic (inferrable), palindromic (not inferrable) or incompatible allele frequencies?
Removing the following SNPs for inco…
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Hello all!
I am trying to assess Runs of Homozygosity in BCFtools for 151 samples contained in a single VCF file.
I have already run the command line:
bcftools roh -G30 –AF-dflt 0.4 NEL_Fabricia.…
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![image001.png](https://waffleio-direct-uploads-production.s3.amazonaws.com/uploads/5759f0b40b37b00e00e7d3d4/125516c66e82c728ace21e0d46e1999b2487d3f9deabf301b44fff9e2c4533317346f67c25dce57ae71528070b0…