arq5x

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

Example

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

arq5x

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

arq5x

#!/usr/bibn/env python

print "hi"

arq5x

# compute a BEDGRAPH RNA-seq coverage across the entire genome for each sample:
bedtools genomecov -bga -split -ibam sample1.sorted.bam > 1.bg
bedtools genomecov -bga -split -ibam sample1.sorted.bam > 2.bg
bedtools genomecov -bga -split -ibam sample1.sorted.bam > 3.bg


# compute the mean coverage at each interval.
bedtools unionbedg -i 1.bg 2.bg 3.bg \
   | awk '{sum=0; for (col=4; col<=NF; col++) sum += $col; print $0"\t"sum/(NF-4+1); }'
chr1 900  1000 0  60 0	20

arq5x

# assumes that the BEDGRAPH is the output of the bedtools genomecov tool using the -bga option.
$ cat foo.bedg
chr1	0	10	5
chr1	10	20	5
chr1	20	30	10
chr1	30	40	11
chr1	40	50	9
chr1	50	60	10
chr1	60	70	11
chr1	70	80	15

arq5x

# test each database file individually
time bedtools intersect -wa -wb -sorted \
                            -a hg19.rmsk.bed.gz \
                            -b hg19.segdup.bed.gz \
                            > /dev/null
real	0m5.069s
user	0m5.007s
sys	0m0.056s

time bedtools intersect -wa -wb -sorted \

arq5x

DIR=bam/t1d-run2a-redo/

# line 10: run flagstats on marked dup BAM
# line 11: grab the number of duplcates line and the total reads line
# line 12 grab the total and dup total
# line 13: place the total followed by duplicate count on same line
# line 14: print the duplicate fraction
for file in `ls $DIR/*.bwamem.sort.dedup.bam`;
do
    samtools flagstat $file | \

arq5x

1. Deanna's biostars post
2. MAPT alt locus
3. MAPT under selection in Eurpeans
4. Zody/Eichler MAPT Inversion toggling
5. The MAPT locus—a genetic paradigm in disease susceptibility
6. Case study for reporting variants in the VCF format.
7. http://content.csbs.utah.edu/~rogers/ant6299/readings/Hardy-BST-33-582.pdf
8. Kitzman/Eichler show that sample NA10847 is heterozygous H1/H2 http://www.nature.com.proxy.its.virginia.edu/nbt/journal/v29/n1/extref/nbt.1740-S1.pdf
9. Terminology

arq5x

# update things
sudo apt-get update

# get postgres up and running
sudo apt-get install postgresql-9.3
sudo apt-get install postgresql-server-dev-9.3
sudo apt-get install postgresql-client
sudo apt-get install postgresql postgresql-contrib
sudo -u postgres psql postgres
\password postgres