I'm doing local ancestry estimations for GWAS data using the LAMP-LD software, I just got the results, which are ranges of ancestry across each chromosome per individual. This is small example of the output for a given chromosome:
00:1935 01:1981 02:50531 00:50937
1: Native American ancestry(red)
0: European ancestry (blue)
2: African ancestry (orange)
00 means that both haplotypes comes from European ancestry,
01 half European and half Native American,
02 half European and half African. The numbers after the semicolon are the number of variants on each haplotype.
I was looking in the web but I haven't found any tool (online or script like in R) that can take that input format and draw a plot like this:
I'll appreciate if you can give some advice
Thanks in advance!