Copy Number Assessment of Population Scale Array-CGH (canny)

Description

This repository contains software that was used to analyze 2135 Agilent 1M CGH arrays designed to assess copy number variation genotypes in Phase 3 samples from the 1000 Genomes Project.

Required third-party resources

A number of third party software packages and modules are required by these programs:

•       R:  http://www.r-project.org/, with LPCM and ggplot2 packages
  

• samtools: https://github.com/samtools/htslib (also contains tabix, bgzip)
• vcftools: http://vcftools.sourceforge.net/

•    perl:  Statistics::R package, http://search.cpan.org/~fangly/Statistics-R-0.32/
  

In addition, you will need:

• tabix indexed file with log2 ratios for each probe and sample -obtainable here ()
• sample list in same order as probe file -obtainable here ()

Example workflow

An example workflow would be as follows:

Input is VCF:

canny.pl \
--input_filename=test.vcf.gz \
--ratio_filename=allData.filtered.gc.txt.corr3.allCols.dat.gz \ 
--sample_filename=samples.txt \
--plot_results \
--bandwidth=0.05 \
--threshold=0.3 \
--output_filename=test.aCGH.genotypes.vcf.gz

Input is Region:

canny.pl \
--input_region=7:143911018-144034817 \
--ratio_filename=allData.filtered.gc.txt.corr3.allCols.dat.gz \
--sample_filename=samples.txt \
--plot_results \
--bandwidth=0.05 \
--threshold=0.3 \
--output_filename=test.aCGH.genotypes.vcf.gz

Contact

Questions: Please contact Ryan Mills at remills@umich.edu 05/05/2014