cth

name	explain-diff-html
description	Use when the user asks for a rich explanation of a code change, diff, branch, or PR. Produces HTML output.

Explain Diff

Please make me a rich, interactive explanation of the specified code change.

It should have these sections:

cth

## Genetic Risk Score power simulator with support for imputed genotypes.
# The motivating idea was to check whether inclusion of (badly) imputed SNPs still improves power.
# Christian Theil Have, 2018.

# Simulated annealing to generate permutation of genotypes that minimizes fn
genetic.optim <- function(genotypes,fn) {
  randomswap <- function(genotypes) {
    i <- sample(length(genotypes),1)
    j <- sample(which(genotypes!=genotypes[i]),1)
    tmp <- genotypes[i]

cth

# A plot similar to upset plots to visualize overlaps between sets

using Plots 

# Where does lines begin/end
function set_line!(set,vals,index)
  start = stop = 0
  for i in 1:length(vals)
    if vals[i] ∈ set
      if start == 0

cth

# Basic julia script for filter INFO in VCF files

using BGZFStreams

# usage: julia filterinfo.jl input.vcf output.vcf INFO
sin = BGZFStream(ARGS[1])
sout = BGZFStream(ARGS[2],"w")
min_info = parse(Float64,ARGS[3]) 
min_maf = parse(Float64,ARGS[4])

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julia> x=zeros(10)
10-element Array{Float64,1}:
 0.0
 0.0
 0.0
 0.0
 0.0
 0.0
 0.0
 0.0

cth

using DataFrames

parse_identifier(x) = parse(Int32,x[4:end])

function read_snps1(file)
	snps = Set{Int32}()
	open(file) do f
		 for l in eachline(f)
			 push!(snps,parse_identifier(chomp(l)))
		end

cth

Extract Dosage Table

A Julia script to extract regions/individuals from imputed data in vcf format as produced by vcf-misc-tools to a dosage table format convenient for asssociation analyses.

The computionally/IO heavy parts are submitted via cluster grid engine via qsub.

Installation

To install type:

cth

#!/home/fng514/bin/julia
#$ -S /home/fng514/bin/julia
#$ -cwd 
#
# Split multi allelic sites:
# 1. Split multi-allelic sites into multiple VCF lines, s.t., a) each line has one unique alternative allele, and b) if person has an other alternative allele than the one specified for the line in question, then that particular genotype is coded as missing in that line.
# 2. Run bi-allelic hardy weinberg test for each of these lines.
# 
# Christian Theil Have, 2016.

cth

#!/home/fng514/bin/julia
#$ -S /home/fng514/bin/julia
#$ -cwd 

# Christian Theil Have, 2016.

using HypothesisTests
using StatsBase

nucleotides = Set{AbstractString}(["A","G","C","T"])

cth

#!/home/fng514/bin/julia
#$ -S /home/fng514/bin/julia
#$ -cwd 

# Christian Theil Have, 2016.

#import GZip 

function process_vcf_line(outfile,line, dpmin, gqmin)
	fields = split(line)