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1 year ago Hej, I have a similar question as Benjamin about $a an $b column in NgsRelate output. I have 19 individuals numbered from individual1 to individual19 but $a start with a value of 0:
head(WADD)
a b nSites J9 J8 J7 J6 J5 J4 J3 J2 J1 rab Fa Fb theta
1 0 1 424664 1.000000 0e+00 0.000000 0 0 0 0 0 0 0.000007 2e-06 2e-06 0.000005
2 0 2 428812 0.992928 2e-06 0.007070 0 0 0 0 0 0 0.007071 0e+00 0e+00 0.003535
3 0 3 489673 1.000000 0e+00 0.000000 0 0 0 0 0 0 0.000009 0e+00 0e+00 0.000005
4 0 4 590884 1.000000 0e+00 0.000000 0 0 0 0 0 0 0.000003 1e-06 2e-06 0.000002
5 0 5 575600 0.964439 3e-06 0.035558 0 0 0 0 0 0 0.035560 0e+00 0e+00 0.017780
6 0 6 588079 1.000000 0e+00 0.000000 0 0 0 0 0 0 0.000005 2e-06 2e-06 0.000003
inbred_relatedness_1_2 inbred_relatedness_2_1 fraternity identity zygosity X2of3_IDB FDiff loglh
1 2e-06 2e-06 0.000000 2e-06 0.000002 0.000007 0e+00 -597341.5
2 0e+00 0e+00 0.007070 0e+00 0.007070 0.007071 0e+00 -622501.2
3 0e+00 0e+00 0.000000 0e+00 0.000000 0.000009 0e+00 -705558.7
4 0e+00 0e+00 0.000001 0e+00 0.000001 0.000005 -1e-06 -888132.5
5 0e+00 0e+00 0.035558 0e+00 0.035558 0.035560 0e+00 -910383.2
6 2e-06 2e-06 0.000000 2e-06 0.000002 0.000005 0e+00 -889309.4
nIter bestoptimll coverage
1 90 -597341.8 0.532331
2 138 -1.0 0.537531
3 58 -705559.0 0.613822
4 91 -888133.0 0.740694
5 110 -1.0 0.721535
6 71 -889309.9 0.737178
X2dsfs
1 2.394796e-01,2.414616e-01,9.230918e-03,1.937839e-01,2.612793e-01,1.350588e-02,1.347052e-02,1.790330e-02,9.885077e-03
2 2.653634e-01,2.179033e-01,8.895433e-03,1.966038e-01,2.543681e-01,1.419341e-02,1.467328e-02,1.979155e-02,8.207748e-03
3 2.334524e-01,2.477280e-01,1.074681e-02,1.899863e-01,2.594139e-01,1.552159e-02,1.546589e-02,1.863968e-02,9.045419e-03
4 2.249027e-01,2.540790e-01,1.474548e-02,1.799104e-01,2.634229e-01,1.848910e-02,1.583578e-02,1.864780e-02,9.966933e-03
5 2.604610e-01,2.168638e-01,1.662494e-02,1.895160e-01,2.538857e-01,1.868943e-02,1.567064e-02,1.924076e-02,9.047746e-03
6 2.284740e-01,2.493034e-01,1.583891e-02,1.822067e-01,2.616735e-01,1.802491e-02,1.673095e-02,1.817321e-02,9.574491e-03
R0 R1 KING X2dsfs_loglike X2dsfsf_niter Pops
1 0.086886 0.533925 0.218230 -650097.6 55 WADD
2 0.092656 0.538846 0.216490 -648797.9 39 WADD
3 0.101046 0.520819 0.208931 -767919.2 35 WADD
4 0.116092 0.525053 0.202671 -969362.2 30 WADD
5 0.127205 0.532696 0.198822 -937745.9 31 WADD
6 0.124468 0.523056 0.198308 -969072.9 27 WADDDoes the '0' correspond to Individual1 and so on, and should I add 1 to all the values in the $a and $b columns? Best, Homère
Hi there,
If this relates to using the sample names in VCF files rather than assigned integers, this would be very helpful.
As a quick sanity check, could you confirm that the output sample naming (0-->N) in the results file is indeed the same as the sample order (left to right) in the input .vcf file. E.g. sample '0' in the results file is the first sample in the .vcf, and sample '1' in the results file is the second sample in the .vcf etc...
Thanks so much.