CSCNPhaser: Inference of Chromosome-Specific Copy Number Using Population Haplotypes

site was last updated 02/10/11

A large number of copy number variations (CNVs) have been identified in humans. In practice, because our human genome is a diploid, most sequencing platforms are limited to (or more accurate) for detecting total copy numbers rather than chromosome-specific copy numbers at each of the two homologous chromosomes. Given a set of total copy numbers and their background haplotypes. the CSCNPhaser aims to infer chromosome-specific copy number using the linkage disequilibrium between CNVs and SNPs.

CSCNPhaser:

	CSCNPhaser is implemented in C.
	Download the program and example input/output files compressed using WinZip Windows Platform Unzip the files using WinZip or other software Usage: double click the CSCNphaser.exe or run the program on DOS prompt Unix Platform (you may need to chmod the program) 1. unzip CSCNphaser_Unix.zip 2. chmod 755 CSCNphaser 3. ./CSCNphaser
	Input file A) CNV.txt ex) CNV_id sample1 sample2 sample3 sample4 sample5 sample6 1 2 2 2 2 3 3 2 2 2 0 3 3 2 *columns are separated by TAB. col1 : CNV-id col2, col3, ... : copy number for each sample B) CNV_info.txt ex) CNV_id Chromosome Start_position End_position 1 chr1 10 20 2 chr5 5 25 *columns are separated by TAB. col1 : CNV-id col2 : chromosome col3 : start position of the CNV col4 : end position of the CNV C) SNP_chrN.txt chrN : all chromosome observed in file "CNV_info.txt" ex SNP_chr1.txt) 0011101111 0011101111 0011101111 0011101110 0011101110 0011101111 0011101111 0011101111 0011101111 1100010001 1100010001 0011101111 ex SNP_chr5.txt) 111010001100111 111010001100111 111010001100111 111010001100111 101101001011100 101101001011100 111010001100111 010010110011011 111010001100111 010010110011011 101101001011100 010010110011011 row1 : sample1 haplotype 1 row2 : sample1 haplotype 2 row3 : sample2 haplotype 1 row4 : sample2 haplotype 2 row5 : sample3 haplotype 1 row6 : sample3 haplotype 2 . . D) SNP_chrN_info.txt chrN : all chromosome observed in file "CNV_info.txt" ex SNP_chr1_info.txt) SNP_id position allele_0 allele_1 1 2 G A 2 3 A G 3 6 C T 4 11 C G 5 12 C G 6 15 A G 7 16 A G 8 18 C T 9 21 C T 10 25 G A ex SNP_chr5_info.txt) SNP_id position allele_0 allele_1 11 1 C T 12 3 A C 13 6 A C 14 8 C A 15 9 A G 16 13 C G 17 16 C G 18 17 C G 19 19 A C 20 20 A C 21 23 C T 22 24 C T 23 28 G A 24 29 A C 25 31 A G *columns are separated by TAB. col1 : SNP-id col2 : position of the SNP col3 : the nucleotide of 0 in file "SNP_chrN.txt" col4 : the nucleotide of 1 in file "SNP_chrN.txt"
	Output file: result.txt ex) CNV_id sample1 sample2 sample3 sample4 sample5 sample6 1 1/1 1/1 1/1 1/1 1/2 2/1 2 1/1 1/1 0/0 1/2 1/2 0/2 *columns are separated by TAB. col1 : CNV-id col2 : the inferred chromosome-specific copy number of sample1 col3 : the inferred chromosome-specific copy number of sample2 col4 : the inferred chromosome-specific copy number of sample3

If you encounter any problem, please contact Yao-Ting Huang (ythuang at cs.ccu.edu.tw)