Local ancestry inference
8/23/2016
armartin@broadinstitute.org

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## Bed files ##
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The LAI calls are in tab-delimited *.bed format and each file has 6 columns:

Column 1: chromosome number [1-22]
Column 2: start physical position of tract, base-0 (bp)
Column 3: end physical position of tract, base-1 (bp)
Column 4: haploid ancestry call of tract 
Column 5: start genetic position of on tract (cM)
Column 6: end genetic position of on tract (cM)

Haploid ancestry tract code:
AFR = African
EUR = European
NAT = Native American
UNK = masked (poorly called regions). These regions correspond to a maximum posterior probability of the ancestry called < 0.9. 

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## Ancestry karyograms ##
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A PDF of every individual's haploid local ancestry calls (derived from bed files).