Aaron Quinlan arq5x

arq5x / basic-exome-outline.sh

Created June 15, 2012 13:35

Exome pipeline for Charles

	##########################################
	# Step 0. setup a list of sample names.
	# Assume that each of your gzipped
	# FASTQ files is named as follows:
	# sample1.1.fq.gz
	# sample1.2.fq.gz
	# sample2.1.fq.gz
	# sample2.2.fq.gz
	# ...
	# sampleN.1.fq.gz

arq5x / diff-file.sh

Created April 13, 2012 18:17

VCF->TPED-PLINK-BED

	# Create SNPs-only subset of the 1000G callset VCF
	$ curl -s http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120316_phase1_integrated_release_version2/ALL.chr22.phase1_release_v2.20101123.snps_indels_svs.vcf.gz \| \
	zcat \| \
	awk '$0 ~ /^#/ \|\| $0 ~ "VT=SNP"' \| \
	gzip > ALL.chr22.phase1_release_v2.20101123.snps_indels_svs.snpsonly.vcf.gz

	# Use VCFTools to convert to TPED
	$ vcftools

	VCFtools (v0.1.8)

arq5x / overlap.sh

Created April 3, 2012 21:47

aparna

arq5x / ka-ching-steps.sh

Created March 21, 2012 00:48

ka-ching your git commit

	# Note, these instructions assume OS X.
	# Alternatives to the afplay command likely exist on
	# other POSIX systems. Google is your friend.

	# NOTE: Obviously, you can put the MP3 file where ever you so desire.


	# 1. Make a new directory called "ka-ching" under /usr/share/
	sudo mkdir /usr/share/ka-ching

arq5x / setup.py

Created March 14, 2012 10:57

pop packaging

	import ez_setup
	ez_setup.use_setuptools()

	import glob
	import os
	import sys
	from setuptools import setup
	from distutils.extension import Extension

	if 'setuptools.extension' in sys.modules:

arq5x / aldskfnaslkvc.sh

Created February 1, 2012 17:54

working with ira

arq5x / python-prototype.py

Created October 30, 2011 17:06

Protoype for detecting overlaps (partial and complete) among N BED/GFF/VCF files

	#!/usr/bin/env python

	from collections import namedtuple, defaultdict
	from pybedtools import BedTool
	import argparse

	Point = namedtuple('Point', ['id', 'pos', 'type'])
	Interval = namedtuple('Interval', ['chrom', 'start', 'end'])

arq5x / get_bam_allele.py

Created October 21, 2011 14:47

Using pybedtools to report a BAM read's allele when it overlaps a SNP

	#!/usr/bin/env python

	"""
	get_bam_allele.py
	Usage: python get_bam_allele.py [BAM] [BED]
	"""

	from pybedtools import BedTool
	import sys

arq5x / test.py

Created September 6, 2011 01:11

test

	from pybedtools import BedTool
	snps = BedTool('../test/data/snps.bed.gz')
	genes = BedTool('../test/data/hg19.gff')

	intergenic_snps = (snps - genes)
	nearby = genes.closest(intergenic_snps,
	d=True,
	stream=True)
	for gene in nearby:
	if int(gene[-1]) < 5000:

arq5x / performance-comparo.sh

Created August 12, 2011 20:09

pybedtools manuscript

	export PBTHOME=/home/arq5x/cphg-home/projects/pybedtools

	shuffle 1094PC0012.bed > a.shuf.full.bed
	shuffle 1094PC0012.bed > b.shuf.full.bed
	head -1000 a.shuf.full.bed > a.shuf.1e3.bed; head -1000 b.shuf.full.bed > b.shuf.1e3.bed
	head -10000 a.shuf.full.bed > a.shuf.1e4.bed; head -10000 b.shuf.full.bed > b.shuf.1e4.bed
	head -100000 a.shuf.full.bed > a.shuf.1e5.bed; head -100000 b.shuf.full.bed > b.shuf.1e5.bed
	head -1000000 a.shuf.full.bed > a.shuf.1e6.bed; head -1000000 b.shuf.full.bed > b.shuf.1e6.bed
	head -10000000 a.shuf.full.bed > a.shuf.1e7.bed; head -10000000 b.shuf.full.bed > b.shuf.1e7.bed
	head -100000000 a.shuf.full.bed > a.shuf.1e8.bed; head -100000000 b.shuf.full.bed > b.shuf.1e8.bed