cth

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

# Script to calculate INFO (approx R-squared) and Allele frequency from a VCF file (with dosages).
# Like the ones produced with https://github.com/cth/vcf-misc-tools
# Christian Theil Have, 2016.
# Use as you see fit, but no warranties.
# Usage: 
# qsub yuvaraj_info.rb my.vcf my.info

cth

#!/home/fng514/bin/julia
#$ -S /home/fng514/bin/julia
#$ -cwd 
#$ -l pe smp 20
# Julia script to to read VCF file and calculate quality and depth statistics (in parallel)
# Christian Theil Have, 2016.

import GZip 

println(string("Reading ",ARGS[1]))

cth

#!/home/fng514/bin/julia
#$ -S /home/fng514/bin/julia
#$ -cwd 
#$ -pe smp 20

# Julia script to read a VCF file and calculate tstv by stepwise GQ and DP tresholds
# Christian Theil Have, 2016.

import GZip 

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 
#
# 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.

#import GZip 

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

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

# A datatype of storing Danish CPR numbers  and accommpanying function for converversion to/from strings

type CPR
	date::Date
	serialnumber::UInt16
end

Base.string(x::CPR) = string( dec(Integer(Dates.Day(x.date)),2), dec(Integer(Dates.Month(x.date)),2), dec(Integer(Dates.Year(x.date)) % 100), "-", dec(x.serialnumber, 4)) 

ismale(x::CPR) = x.serialnumber % 2 == 1

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)

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"])