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.
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 ()
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
Questions: Please contact Ryan Mills at [email protected] 05/05/2014