GitHub - tinathu/msg: Multiplexed Shotgun Genotyping

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 23 Commits
R.methodsS3		R.methodsS3
R.oo		R.oo
cmdline		cmdline
doc		doc
example		example
README		README
breakpoint-widths.R		breakpoint-widths.R
countalleles.c		countalleles.c
ded.R		ded.R
extract-ref-alleles.py		extract-ref-alleles.py
fastq_2_fasta.pl		fastq_2_fasta.pl
filter-sam.py		filter-sam.py
fit-hmm.R		fit-hmm.R
hmmlib.R		hmmlib.R
hmmprobs.c		hmmprobs.c
make-pileups.sh		make-pileups.sh
makefile		makefile
mapping_functions.py		mapping_functions.py
msg.pl		msg.pl
msgCluster.pl		msgCluster.pl
msglib.py		msglib.py
parent1or2-hmm.sh		parent1or2-hmm.sh
parse_BCdata2BWA.pl		parse_BCdata2BWA.pl
parse_and_map.py		parse_and_map.py
plot_error.R		plot_error.R
reformatFasta4sam.pl		reformatFasta4sam.pl
summaryPlots.R		summaryPlots.R
summary_mismatch.pl		summary_mismatch.pl
updateRef.pl		updateRef.pl
write-hmm-data.R		write-hmm-data.R

Repository files navigation

MSG: Multiplexed Shotgun Genotyping
http://genomics.princeton.edu/AndolfattoLab/MSG.html
https://github.com/tinathu/msg
http://www.ncbi.nlm.nih.gov/pubmed/21233398

### Dependencies ###
Python (2.6.4) 
bwa (0.5.7)
samtools (0.1.9-3)
biopython-1.53
Pyrex-0.9.9
pysam-0.1.2 (apply fix as described here: http://code.google.com/p/pysam/issues/detail?id=22&can=1&q=dandavison0)
R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 1.2.0 and R.oo 1.7.3)

### Installation instructions ###
git clone git@github.com:tinathu/msg.git
cd msg
make