The .lanc Format

lanctools is built around the .lanc file format introduced by Hou et. al. This is a compressed format which uses a breakpoint-encoded representation of phased local ancestry data.

Rather than storing ancestry at every variant, each individual is represented as a sequence of ancestry tracts. Each tract records the 0-based index where the tract ends (exclusive) and the phased local ancestry state in that interval.

Local Ancestry Array

The dense representation corresponds to an array of shape \((n, p, 2)\), where:

\(n\) is the number of samples
\(p\) is the number of variants
The final dimension corresponds to the two phased haplotypes (ploidy=2)

The ancestry values in this array are coded as integers corresponding to the admixing populations in the sample.

File Format

The first line contains:

p n

where \(p\) is the number of variants and \(n\) is the number of samples. This is followed by exactly \(n\) lines, one per individual.

Each individual line consists of one or more ordered breakpoint records, separated by spaces. Each breakpoint record has the form:

<stop>:<anc0><anc1>

where

stop is the exclusive ending variant index of the current ancestry tract
anc0 is the ancestry (integer-coded) at haplotype 0
anc1 is the ancestry (integer-coded) at haplotype 1

Example

The following is a .lanc file for 4 variants and 3 samples.

4 3
1:00 4:10
4:11
1:01 2:11 3:10 4:00

The corresponding dense matrices for haplotype 0 is:

\[\begin{pmatrix} 0 & 1 & 1 & 1\\ 1 & 1 & 1 & 1\\ 0 & 1 & 1 & 0 \end{pmatrix}\]

And for haplotype 1:

\[\begin{pmatrix} 0 & 0 & 0 & 0\\ 1 & 1 & 1 & 1\\ 1 & 1 & 0 & 0 \end{pmatrix}\]

Limitations

The .lanc format has several limitations which may be addressed in future work.

It can represent a maximum of 10 ancestries
It cannot represent missing data
It can only represent autosomes