#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Individual1 Individual2 Individual3 Individual4 Individual5 Individual6
22 10000 ID1 A G 0 PASS GT 0|1 0|1 0|1 1|1 1|1 1|1
22 10001 ID2 A G 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10002 ID3 A G 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10003 ID4 G A 0 PASS GT 1|0 1|0 1|0 1|0 1|1 1|1
22 10004 ID5 A G 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10005 ID6 A G 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10006 ID7 A G 0 PASS GT 0|1 0|1 0|1 1|1 1|1 1|1
22 10007 ID8 A G 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10008 ID9 C T 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10009 ID10 C T 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10010 ID11 A G 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10011 ID12 C T 0 PASS GT 0|1 0|1 0|1 1|0 1|1 1|1
22 10012 ID13 C A 0 PASS GT 1|0 1|0 1|0 1|0 1|1 1|1
22 10013 ID14 T G 0 PASS GT 1|0 1|0 1|0 1|0 1|1 1|1
22 10014 ID15 G A 0 PASS GT 1|0 1|0 1|0 1|0 1|1 1|1
I need to calculate the average fraction of 'ID' that are identical, averaged across all possible pairings (Individual1,Individual2), (Individual1,Individual3), (Individual1,Individual4),
This is averaged over all ID, and reported for all pairs of individuals. In this file, I have over 2000 IDs and several individuals and am currently doing it in excel. Is this possible to code this formula in bash or python at all to accept a text tab delimited file ?
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