Ayton Meintjes ameintjes

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command	description
ctrl + a	Goto BEGINNING of command line

This gist lets you keep IPython notebooks in git repositories. It tells git to ignore prompt numbers and program outputs when checking that a file has changed.

To use the script, follow the instructions given in the script's docstring.

For further details, read this blogpost.

The procedure outlined here is inspired by this answer on Stack Overflow.

Clone this gist into the working directory

git clone [email protected]:96670d2eb66a8ad9854b6f52a2b5339c.git vagrant-ansible-neo
cd vagrant-ansible-neo

Install the neo4j role into the working directory

ansible-galaxy install julienroubieu.neo4j -p .

Bring up the vagrant box

Preimputation steps

Read the Sanger How-to page to make sure your vcf file meets all the requirements for Sanger imputation.

The preimputation steps for UMichigan and Sanger are relatively similar. The main difference is that VCF files are not split by chromosome under sanger imputation. I recommend carrying out the Michigan preimputation steps anyways. If you have already carried out the preimputation steps for U Mich imputation then the only other requirement will be to merge the chr.vcf files into one vcf file and sort the result.

#merge vcf files from list of files
bcftools concat --file-list ~/preimputation/vcf_list.txt -o merged.vcf
gzip merged.vcf

	# Last updated May, 2024 for Apple silicon Macs
	# Install Homebrew if you don't already have it: https://brew.sh

	# install nano from homebrew
	brew install nano nanorc

	# update your nanorc file
	echo 'include "'"$(brew --cellar nano)"'//share/nano/.nanorc"' >> ~/.nanorc

	# close and re-open your terminal and you'll have syntax highlighting

	def explode_hstore(df, column):
	"""Explode a column of a dataframe containing PostgreSQL hstore k-v pairs in the format of:

	"foo"=>"bar", "baz"=>"quux", ...

	Every key becomes a column. If a given row's pairs doesn't have a key, then the resulting column's value
	will contain NaN.
	"""
	# split the tags column out as a new series, and break up each k=>v pair
	s = df[column].str.split(', ').apply(pd.Series, 1).stack()

	Byobu is a suite of enhancements to tmux, as a command line
	tool providing live system status, dynamic window management,
	and some convenient keybindings:

	F1 * Used by X11 *
	Shift-F1 Display this help
	F2 Create a new window
	Shift-F2 Create a horizontal split
	Ctrl-F2 Create a vertical split
	Ctrl-Shift-F2 Create a new session

	#!/bin/bash

	## Wrapper to interact with NCBI SRA using aspera ascp command line interface
	## v 2.5 \| 04/2017
	## @sbamin

	# More info: http://download.asperasoft.com/download/docs/ascp/2.7/html/

	# usage
	show_help() {

	{
	"mongod_log": {
	"title": "MongoDB server log format",
	"regex": {
	"main": {
	"pattern": "^(?<timestamp>\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}[,\\.]\\d+\\+\\d+)\\s+(?<level>\\w)\\s+(?<component>\\w+\|-)\\s+\\[?(?<context>-?\\w+)?\\]\\s+(?<body>.*)$"
	}
	},
	"level": {
	"critical": "F",

	*bcftools filter
	*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
	qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

	*printing out info for only 2 samples:
	bcftools view -s NA20818,NA20819 filename.vcf.gz

	*printing stats only for variants passing the filter:
	bcftools view -f PASS filename.vcf.gz