Sean Ephraim sephraim

sephraim / set_extension.rb

Created November 11, 2016 18:55

Automatically set output file extension

__F_OUT__ = __F_IN__.sub(/(\.[^.]+$)|$/, '.out')

sephraim / init_or_incr.rb

Last active November 12, 2016 01:18

Initialize or increment an integer variable

n = n ? n + 1 : 1

sephraim / mount_smb.sh

Last active November 12, 2016 01:16

Mount / unmount SMB file share on Mac OS X

	# 1. Create the mount point
	mkdir share_name

	# 2. Mount the share
	mount_smbfs //username:password@server.name/share_name share_name/

	# 3. Unmount the share
	umount share_name

sephraim / create_tar_gz.sh

Last active November 11, 2016 22:54

Create tar.gz file

tar -cvzf __OUTPUT__.tar.gz __INPUT__

sephraim / remove_VCF_duplicates.sh

Last active September 11, 2024 04:41

Remove duplicate variants from VCF file

	#!/bin/bash

	myvcf="$1"

	# Print header
	bcftools view -h -O v "$myvcf"

	# Sort and remove duplicates per chromosome
	for i in {1..22} MT X Y
	do

sephraim / check_utils.sh

Created November 11, 2016 23:18

Check if bash utilities are installed

	for util in 'awk' 'ruby' 'python' 'faketool'
	do
	if [ -z $(which "$util" 2> /dev/null) ]; then
	echo "ERROR: $util is not in your \$PATH" >&2
	exit 1
	fi
	done

sephraim / add_user.sh

Created November 11, 2016 23:56

Add new user (CentOS)

	# Add user and user's full name and groups
	useradd -m -c '__FULL_NAME__' -g __PRIMARY_GROUP__ -G __SECONDARY_GROUPS__ __USERNAME__

	# Set user's password
	passwd __USERNAME__

sephraim / multi_qsub_submit.sh

Last active November 12, 2016 01:05

Submit multiple qsub jobs quickly

	#!/bin/bash

	# Submit a job for each chromosome
	# Job logs will be named __JOB_NAME__.chr1.o, __JOB_NAME__.chr2.o, etc.
	for chr in {1..22} MT X Y
	do
	qsub -N __JOB_NAME__.chr$chr -v CHR=$chr qsub.sh
	done

sephraim / sort_vcf.sh

Last active November 14, 2016 04:39

Sort a VCF (using bcftools + bash)

	##
	# Sort a VCF
	#
	# Input:
	# vcf[.gz] or bcf[.gz]
	# Output:
	# vcf
	#
	# Example usage:
	# ./sort_vcf.sh my.[vcf\|bcf][.gz] > my.sorted.vcf

sephraim / vcf_la_norm.sh

Last active November 14, 2016 04:41

Left-align / normalize a VCF

bcftools norm -f ~/data/references/human_g1k_v37.fa -c s -m- -O v __INPUT__ | awk -F'\t' '$5 !~ ","' | bgzip -c > __OUTPUT__