nievergeltlab’s gists

nievergeltlab / ambiguous_alleles.sh

Last active July 25, 2017 18:42

Get ambiguous alleles

	#Assumes data is a table delimited .bim file
	bimfile=bim_name_here
	grep -P "A\tT" $bimfile > ambiguous_snps.txt
	grep -P "T\tA" $bimfile >> ambiguous_snps.txt
	grep -P "C\tG" $bimfile >> ambiguous_snps.txt
	grep -P "G\tC" $bimfile >> ambiguous_snps.txt


	#for metal
	bimfile=LOOMeur_1_.results

nievergeltlab / forest_plot

Last active February 14, 2017 20:15

Forest plot for meta-analysis in R

	library(metafor)

	y <- scan(what=numeric())
	0.273936
	0.278002
	0.117789
	0.170343

	se <- scan(what=numeric())
	0.0864617

nievergeltlab / make_dos.pbs

Last active April 4, 2017 20:10

This makes imputed probabilities from ricopili into a dosage file format Working with job system (TORQUE). Have a list of files. Want to run same operation on all of them. Can run multiple at the same time on a single node The files to be processed are listed in a single file. The number of processes to be run on a single node are noted. The job…

	#PBS -lnodes=1
	#PBS -lwalltime=0:05:00

	#!/bin/bash

	while getopts n:o:p:d:s: option
	do
	case "${option}"
	in
	o) outputfile=${OPTARG};;

nievergeltlab / analyze_snp_in_R.r

Last active June 29, 2021 21:12

User R to analyze a single SNP from PLINK. The SNP is analyzed using an ordered logit model, with the SNP as an outcome (usually it's done as OLS or logistic with the SNP as a predictor).

	#Test the association between a SNP and PTSD, in R, assuming ordered logit of the SNP

	#Do the following in PLINK
	plink --bfile --snp rs4680 --recodeA --out rs4680

	#Open the corresponding .raw file and note the column name for the SNP. you'll need this for R

	#Then load R

	R

nievergeltlab / qq_plot.pbs

Last active November 2, 2017 18:44

QQ plot function. v2 reads data using the data.table library

	#!/bin/bash

	while getopts s:i:o:e: option
	do
	case "${option}"
	in
	s) scriptname=${OPTARG};;
	i) indata=${OPTARG};;
	o) outdata=${OPTARG};;
	e) errorbars=${OPTARG};;

nievergeltlab / manhattan_plot.r

Last active May 1, 2017 18:51

Manhattan Plots V2 of the plotter will color SNPs within a set kb window of any hits

	args <- commandArgs(trailingOnly = TRUE)
	scriptloc <- args[1]
	results <- args[2]
	outfile <- args[3]
	snpcol <- args[4]
	chrcol <- args[5]
	bpcol <- args[6]
	pcol <- args[7]

nievergeltlab / name_chromosome_chunk.sh

Created March 13, 2017 16:18

Get chromosome number and chunk number from file name. For ricopili.

	chunknum=$(echo $chunk \| sed 's/.$chr[0-9]_[0-9]_[0-9]$.*/\1/')
	chrnum=$(echo $chunk \| sed 's/.$chr[0-9]$.*/\1/')

nievergeltlab / ibd_compare

Created March 22, 2017 22:08

2 file IBD, if strand mismatches and allele mismatches

	bimfile=pts_meg2_mix_am-qc.bim
	grep -P "A\tT" $bimfile > ambiguous_snps.txt
	grep -P "T\tA" $bimfile >> ambiguous_snps.txt
	grep -P "C\tG" $bimfile >> ambiguous_snps.txt
	grep -P "G\tC" $bimfile >> ambiguous_snps.txt


	#filer out ambiguous
	$plink_location --bfile pts_meg2_mix_am-qc --exclude ambiguous_snps.txt --make-bed --out pts_meg2_mix_am-qc-ambig

nievergeltlab / analyze_dosages.pbs

Last active April 4, 2017 19:59

Analyze dosages data from Ricopili

	#PBS -lnodes=1
	#PBS -lwalltime=0:05:00

	#!/bin/bash

	while getopts a:b:o:p:d: option
	do
	case "${option}"
	in
	a) phenotype=${OPTARG};;

nievergeltlab / extract_snp_from_dosages

Created March 24, 2017 18:23

Algorithm: Find which file the SNP is in, then zgrep the SNP out. This script will output a .dosage file for each snp in the list. to combine them into a file, it's of course just a matter of using "cat"

	#Requires a list of SNPs written into snplist.txt

	dosage_directory=write_path_to_dosage_files_here
	for snp in $(cat snplist.txt)
	do
	filename=$(grep -w -m1 -l $snp "$dosage_directory"/*.map \| sed 's/.map/.gz/g' )
	zgrep -w -m1 $snp $filename > "$snp".dosage
	done

	chunknum=$(echo $chunk \| sed 's/.\(chr[0-9]_[0-9]_[0-9]\).*/\1/')
	chrnum=$(echo $chunk \| sed 's/.\(chr[0-9]\).*/\1/')

Adam X. Maihofer nievergeltlab