README: bam2cnv

bam2cnv is a set of tools (written by Heng Li)  which create a cnv filter, used in the SGDP project.

The initial input is actually a vcf (rather than a bam). To run the scripts for each sample, do the following:

k8 cnv_cbs.js depth.txt > seg.bed
k8 cbs2bed.js seg.bed > flt.bed

Here "depth.txt" gives the read depth at SNP/INDEL sites. Each line consists of snp_chr, snp_pos and read depth at the position. Script cnv_cbs.js uses the Circular Binary Segmentation (CBS) algorithm to cluster SNPs/INDELs with similar copy number. "cbs2bed.js" finds a cut and generates regions that should be filtered out.