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Question: Is there a tool to draw local ancestry plots per chromosome?
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Dear biostars:

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!

ADD COMMENTlink 4.3 years ago bibb77 • 50 • updated 3.3 years ago michael.wathen • 0
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Hello, Did you ever find a R script or another visualization tool which would enable you to graph your LAMP-LD output? I have the same output format which I would like to graph. Thank you.

ADD REPLYlink 2.0 years ago
genomics Newbie
• 20
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Hello,

I was wondering if you were able to successfully find what you were looking for.

Michael

ADD COMMENTlink 3.3 years ago michael.wathen • 0
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Hello Michael,

I have the same question as above and have not found any R plots or graphing software for LAMP-LD results. Do you have any recommendations?

Thank you.

ADD REPLYlink 2.1 years ago
genomics Newbie
• 20

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