how do I decide which individuals to remove in plink.genome in IBD analysis?

Question

[anamaria]

Hello,

I was running this command:

plink --bfile output4 --genome --genome-full --min 0.25

and I got the output bellow. Can you please tell me how to decide which individuals to remove?

Thanks Ana

     FID1   IID1     FID2   IID2 RT    EZ      Z0      Z1      Z2
 PI_HAT PHE       DST     PPC   RATIO    IBS0    IBS1    IBS2  HOMHOM
HETHET
   fam1054  G1054  fam1054   G700 OT     0  0.0045  0.9918  0.0037
0.4996  -1  0.839150  1.0000 209.7368     103  118630  250667 19.0000
3985.0000
   fam1054  G1054  fam1054   G701 OT     0  0.0035  0.9965  0.0000
0.4982  -1  0.838381  1.0000 266.0667      81  119124  249829 15.0000
399 1.0000
  fam1079  G1079  fam2484  G2484 UN    NA  0.0000  0.0007  0.9993
0.9997  -1  0.999889  1.0000      NA       0      82  370250  0.0000
4591.0000
  fam1245  G1237  fam1245  G1245 OT     0  0.0036  0.9955  0.0009
0.4986  -1  0.838770  1.0000 188.4762      83  118647  249728 21.0000
3958.0000
  fam1245  G1241  fam1245  G1245 OT     0  0.0042  0.9834  0.0124
0.5041  -1  0.840569  1.0000 265.8667      97  117116  250690 15.0000
3988.0000
  fam0176   G174  fam0176   G176 OT     0  0.0047  0.9953  0.0000
0.4977  -1  0.837799  1.0000 190.0476     107  118306  246937 21.0000
3991.0000
  fam0176   G175  fam0176   G176 OT     0  0.0045  0.9889  0.0066
0.5011  -1  0.839611  1.0000 198.6500     102  117026  248327 20.0000
3973.0000
  fam0179   G177  fam0179   G179 OT     0  0.0091  0.9883  0.0026
0.4968  -1  0.838517  1.0000 116.5000     207  117568  247532 34.0000
3961.0000
  fam0179   G178  fam0179   G179 OT     0  0.0098  0.9893  0.0009
0.4955  -1  0.838160  1.0000 90.4318     224  117440  246548 44.0000
3979.0000
  fam1818  G1818  fam1818  G1819 OT     0  0.0050  0.9864  0.0086
0.5018  -1  0.839882  1.0000 208.8947     115  117679  250401 19.0000
3969.0000
  fam1818  G1818  fam1818  G1820 OT     0  0.0050  0.9937  0.0013
0.4982  -1  0.838709  1.0000 208.6842     115  119083  250671 19.0000
3965.0000
  fam2450  G2007  fam2450  G2450 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.831786  1.0000 79.0196     278  120248  238553 51.0000
4030.0000
  fam2450  G2024  fam2450  G2450 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.832052  1.0000 104.6750     242  118317  235124 40.0000
4187.0000
  fam2181  G2181  fam5745  G5745 UN    NA  0.0002  0.0034  0.9964
0.9981  -1  0.999402  1.0000      NA       4     432  367475  0.0000
4613.0000
  fam2183  G2183  fam2183  G2184 OT     0  0.0057  0.9816  0.0126
0.5034  -1  0.840452  1.0000 164.9583     133  117858  252192 24.0000
3959.0000

Answer 1

[Sam]

You can use the --grm-cutoff to remove related sample with plink. Alternatively, you can use my GreedyRelated software to take into account of sample phenotype when you remove related samples

[anamaria]

--grm-cutoff is flag for GCTA? How would I use it given my Plink files?

[Sam]

That is also a flag in PLINK 1.9 called --grm-cutoff

[anamaria]

can you please share with me how I can run this on my plink output4.bim... files

[Sam]

plink --bfile output4 --genome --grm-cutoff 0.25

[anamaria]

Hi Sam,

thanks for getting back to me! So I was running this:

plink --bfile output4 --genome --grm-cutoff 0.25 --make-bed --out output5

so can I conclude that in my output5 I have individuals with Pihat < 0.25?

Thanks Ana

[Sam]

yup, document is here: https://www.cog-genomics.org/plink/1.9/distance#rel_cutoff