Entering edit mode
4.6 years ago
anamaria
▴
220
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
--grm-cutoff is flag for GCTA? How would I use it given my Plink files?
That is also a flag in PLINK 1.9 called --grm-cutoff
can you please share with me how I can run this on my plink output4.bim... files
Hi Sam,
thanks for getting back to me! So I was running this:
so can I conclude that in my output5 I have individuals with Pihat < 0.25?
Thanks Ana
yup, document is here: https://www.cog-genomics.org/plink/1.9/distance#rel_cutoff