Breakpoints
Breakpoints files (.bp files) store your samples’ local ancestry labels. Each line in the file denotes the ancestral population (ex: YRI or CEU) of a portion of a chromosomal strand (or haplotype block) of an individual.
The set of haplotype blocks for an individual are delimited by a sample header of the form {sample}_1 (for the first chromosomal strand) or {sample}_2 (for the second chromosomal strand). Blocks from {sample}_1 must be directly followed by blocks from {sample}_2.
Each set of haplotype blocks follows a tab-delimited format with the following fields. Lines within a sample’s set of blocks must be sorted according to chrom, bp, and cm - in that order.
Name |
Type |
Description |
|---|---|---|
pop |
string |
The population label of this haplotype block (ex: CEU or YRI) |
chrom |
string |
The name of the chromosome to which this haplotype block belongs (ex: chr1) |
bp |
integer |
The base-pair position of the end of the haplotype block (ex: 1001038) |
cm |
float |
The centimorgan position of the end of the haplotype block (ex: 43.078) |
Examples
See tests/data/outvcf_test.bp for an example of a short breakpoint file:
Sample_1_1 YRI 1 59423086 85.107755 CEU 1 239403765 266.495714 YRI 2 229668157 244.341689 Sample_1_2 YRI 1 59423086 85.107755 YRI 1 239403765 266.495714 CEU 2 229668157 244.341689 Sample_2_1 CEU 1 59423086 85.107755 YRI 1 239403765 266.495714 CEU 2 229668157 244.341689 Sample_2_2 CEU 1 59423086 85.107755 CEU 1 239403765 266.495714 YRI 2 229668157 244.341689
See tests/data/simple.bp for a longer example:
HG00096_1 YRI 1 10122 1.23 HG00096_2 CEU 1 10115 1.2 YRI 1 10116 1.21 ASW 1 10120 1.22 YRI 1 10122 1.23 HG00097_1 YRI 1 10122 1.2 HG00097_2 YRI 1 10115 1.2 CEU 1 10116 1.21 YRI 1 10122 1.23 HG00099_1 YRI 1 10116 1.2 CEU 1 10118 1.22 YRI 1 10122 1.23 HG00099_2 YRI 1 10122 1.23 HG00100_1 ASW 1 10115 1.2 CEU 1 10116 1.21 YRI 1 10120 1.22 CEU 1 10122 1.23 HG00100_2 YRI 1 10114 1.2 CEU 1 10116 1.21 YRI 1 10122 1.23 HG00101_1 YRI 1 10121 1.23 ASW 1 10122 1.23 HG00101_2 YRI 1 10115 1.2 CEU 1 10116 1.21 YRI 1 10120 1.22 ASW 1 10122 1.23