File Conversions
The convert command is used to convert output from a local ancestry
inference tool into the .lanc format. Currently supported formats
are FLARE and RFMix.
Example
lanctools convert --input chr1.anc.vcf.gz --plink chr1 --format FLARE --output chr1.lanc
Arguments
| Option | Argument | Type | Description |
|---|---|---|---|
--input |
TEXT | required | The input local ancestry file |
--plink |
TEXT | required | The corresponding plink2 file prefix |
--format |
TEXT | required | The input file format ("RFMix" or "FLARE") |
--output |
TEXT | required | The output .lanc file |
Note
For --format RFMix, the --input file should be RFMix's .msp.tsv output file, which contains the most likely assignment of subpopulations per CRF point. For --format FLARE, the --input file should be the .anc.vcf.gz file output by FLARE.
Info
Since not all positions in the plink2 files may exist in the FLARE input files, it is necessary to interpolate between positions. We use linear interpolation. This means that if e.g. the .vcf.gz file reports ancestry A for a given haplotype at chr1:100 and ancestry B at chr1:200, we assign ancestry A to all variants in chr1:100-150 and B to all variants from in chr1:150-200.