arq5x’s gists

arq5x / workflow.sh

Last active December 23, 2015 05:39

irradiated clones

	############################################################
	# Novoalign
	############################################################
	export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa.novo.k14.s1.idx
	export IRCHOME=/net/midtier18/vol79/cphg-quinlan2/projects/irradiated-clones
	export STEPNAME=ircnovo
	export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=32000m:ncpus=16 -N $STEPNAME -m bea -M arq5x@virginia.edu";

	echo "cd $IRCHOME; novoalign -d $GENOME -o SAM $'@RG\tID:parental\tSM:parental' -r Random \
	-f fastq/CgmW_AGTCAA_L001_R1.fastq.gz fastq/CgmW_AGTCAA_L001_R2.fastq.gz \

arq5x / flatten_transcripts.py

Created December 4, 2013 15:52

Flattened CCDS

	import pybedtools as pbt
	import sys

	def merge_gene(lines):
	tmp = pbt.BedTool(lines, from_string=True).merge(nms=True)
	print tmp

	gene_lines = ''
	curr_gene = None
	prev_gene = None

arq5x / chromsweep-scalability.sh

Last active December 31, 2015 01:19

Bedtools protocols.

	# /home/arq5x/cphg-home/projects/bedtools-curr-prot-bx

	#######################################################
	# 1. Create subsamples of BAM file and convert to BED.
	#######################################################
	bedtools bamtobed -i ~/cphg-quinlan/projects/rs-exome/bam/1478PC0009B.conc.on.pos.bam \| \
	cut -f 1-3 \
	> datasets/sample.100M.bam.bed &

	samtools view -us 0.10 ~/cphg-quinlan/projects/rs-exome/bam/1478PC0009B.conc.on.pos.bam \| \

arq5x / cell-line-workflow.sh

Last active December 31, 2015 21:39

Ovarian cancer chemoresistance.

	export SAMPLES="2484-AJ-0001 2484-AJ-0002 2484-AJ-0003"

	######################################
	# Make FASTQ
	######################################
	export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
	export STEPNAME=ovc-fastq
	for sample in `echo $SAMPLES`
	do
	export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M arq5x@virginia.edu";

arq5x / AFS_analysis_for_311_samples.ipynb

Last active January 2, 2016 01:39

T1D-RA targeted regulatory sequencing

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arq5x / macs.sh

Last active August 29, 2015 13:56

Examples for generating haplotypes with Macs

	DL: https://code.google.com/p/macs/

	# simulate:
	# 100 individuals (200 haplotypes)
	# "genome" is 1Mb (1e6)
	# mutation and recombinaytion rate at 0.001
	macs 200 1e6 -T -t .001 -r .001 > 200.macs

	# peak at file:
	grep SITE: 200.macs \| head

arq5x / cadd_compress.sh

Last active March 30, 2017 09:09

Various attempts at compressing the raw CADD datasets for use with GEMINI (and by others).

	# Download the raw CADD TSV and Tabix index (no annotations, just scores)
	wget http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz
	wget http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz.tbi

	# it is big. 79Gb
	ls -ltrh whole_genome_SNVs.tsv.gz
	-rw-r--r-- 1 arq5x users 79G Sep 26 01:44 whole_genome_SNVs.tsv.gz

	# for testing, let's play with the chr22 intervals
	tabix whole_genome_SNVs.tsv.gz 22 \| bgzip > whole_genome_SNVs.tsv.22.gz

arq5x / inheritance_scenarios.md

Last active March 28, 2022 21:45

mendelian violations

dad	mom	kid	Inheritance description
HOM_REF	HOM_REF	HOM_REF	Expected
HOM_REF	HOM_REF	HET	Mendelian violation (plausible de novo)
HOM_REF	HOM_REF	HOM_ALT	Mendelian violation (implausible de novo)
HOM_REF	HOM_ALT	HOM_REF	Mendelian violation (uniparental disomy)
HOM_REF	HOM_ALT	HET	Expected
HOM_REF	HOM_ALT	HOM_ALT	Mendelian violation (uniparental disomy)
HOM_REF	HET	HOM_REF	Expected
HOM_REF	HET	HET	Expected

arq5x / summary.md

Last active August 29, 2015 13:57

Discrepancies in PolyPhen2 predictions.

Example

Nonsynonymous change in question (human, build 37; 1-based coordinate)
chrom: chr22 
pos:   24379402
ref:   T
alt:   G

arq5x / go.sh

Created April 9, 2014 18:15

Track Github repo release download info , etc.

curl -i https://api.github.com/repos/arq5x/bedtools2/releases