I am running LAMPHAP, a software to infer local ancestry in admixed genomes, using phased genome-wide SNP data.
As a test I run LAMPHAP with default parameters. The output looks fine (which that I mean the result) but when I was checking the stdout file (that is the file that was generated in the terminal) I couldn't understand this part (from analysis of chromosome 1 of my sample):
removing chunks smaller than 2000000 SNPs
removing 0 (900 1200)
removing 0 (2100 2700)
removing 0 (3000 3300)
removing 1 (900 1200)
removing 1 (2700 3000)
removing 1 (3300 3900)
removing 1 (13200 13500)
removing 1 (18900 19200)
removing 1 (28800 29100)
removing 2 (11400 11700)
.
.
.
The software infers local ancestry using windows, the default parameter for a window is 300 SNP, so I understand that it is somehow removing windows located at those positions. But then why the first line of "removing chunks smaller than 2 million SNPs"? Chromosome 1 on my sample has less thank 60k SNPs. And why is it removing those windows in the first place? I checked the paper and manual but couldn't find an answer. Perhaps I missed something?
Any help would be greatly appreciated.
