HMMcopy

HMMcopy Copy number prediction with correction for GC and mappability bias for HTS data
Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for further analysis. Designed for rapid correction of high coverage whole genome tumor and normal samples.

Author: Daniel Lai, Gavin Ha, Sohrab Shah

We conducted an analysis using our sample datasets with HMMcopy.

• Request and download software from : Shah Lab Download

• follow the instructions on the page to unzip the downloaded file, cmake and make

• three files are required to begin the analysis : readCounts, gc and a mapping files.

• gc content and mapping files for hg18 and hg19 are provided in the tar ball which you downloaded.

• for generating the readCounts file from the BAM file we used :
  bin/readCounter > tum_reads.wig bin/readCounter > norm_reads.wig

• R file provided for analysis can be found at: HMMcopy.R

• 3 plotting functions are provided by HMMcopy - The three plots produced for our data are given here

![] (https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/master/image/plotBias.png)

![] (https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/master/image/plotCorrection.png)

![] (https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/master/image/plotDefaultSegments.png)