No description, website, or topics provided.
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
README.md
canny.pl

README.md

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:

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