arq5x

# compile
$ g++ zlib-example.cpp -lz -o zlib-example

# run
$ ./zlib-example
Uncompressed size is: 36
Uncompressed string is: Hello Hello Hello Hello Hello Hello!

----------

arq5x

echo "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHuvecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmK562HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhekHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhlfHMM.bed.gz" \
> chromhmm-files.txt

arq5x

cat a.bed
chr1	10	50	10

cat b.bed
chr1	20	40	20

cat c.bed
chr1	30	33	30

# Find the sub-intervals shared and unique to each file.

arq5x

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

# assumes you have SSH'ed and qlogin'ed
cd thu
cd mydata

# slide 5
curl https://s3.amazonaws.com/gemini-tutorials/trio.trim.vep.vcf.gz > trio.trim.vep.vcf.gz
curl https://s3.amazonaws.com/gemini-tutorials/dominant.ped > dominant.ped
gemini load --cores 2 \
              -v trio.trim.vep.vcf.gz \
              -t VEP \

arq5x

chr1  10

arq5x

Load a GEMINI database from a VCF

$ gemini load -v nobel.vcf -t VEP --cores 23 -p samples.ped nobel.db

Launch the GEMINI web server

(this will run on your local machine on port 8088)

$ gemini browser nobel.db

arq5x

############################################################
# Index the position-sorted BAM files.
############################################################
export SAMPLES="T10AA T10AB T10D T10H"
export TUMHOME=/home/arq5x/cphg-home/projects/navin-tumor-heterogeneity/
export STEPNAME="bam-index"
for sample in `echo $SAMPLES`
do
export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -N $STEPNAME -m bea -M arq5x@virginia.edu"
      echo "cd $TUMHOME; samtools index bam/$sample.*.bam" | $QSUB

arq5x

import sys

class Line(object):
	def __init__(self, line):
		self.fields = line.split('\t')
		self.chrom = self.fields[0]
		self.start = int(self.fields[1])
		self.end = int(self.fields[2])
		self.depth = int(self.fields[3])

arq5x

export GENOME=hg19
export SNPBUILD=131
curl -s http://hgdownload.cse.ucsc.edu/goldenPath/$GENOME/database/snp$SNPBUILD.txt.gz | \
        zcat | \
        cut -f 2,3,4,5,6,7,10,16 > dbsnp.$SNPBUILD.$GENOME.bed

head dbsnp.$SNPBUILD.$GENOME.bed
chr1	10433	10433	rs56289060	0	+	-/C	near-gene-5
chr1	10491	10492	rs55998931	0	+	C/T	near-gene-5
chr1	10518	10519	rs62636508	0	+	C/G	near-gene-5