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"
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