mismatch allele problem

[luca sclisizzo]

Hello, I'm training to perform GWAS with PLINK. I'm trying to do the PCA with this script 1 (the link to the script on my GitHub). When I run it, the console tells me "Warning: 648750 --score file entries were skipped due to mismatching allele codes. Error: No valid variants in --score file." I can't understand where is the issue. Do you have any ideas?

Thank you,

Luca

[Christopher Chang]

Please post full .log file(s) when asking for troubleshooting help.

[luca sclisizzo]

PLINK v2.00a5.12LM AVX2 Intel (25 Jun 2024)    www.cog-genomics.org/plink/2.0/
(C) 2005-2024 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to sample_results.clean_projected.log.
Options in effect:
  --bfile sample_data.clean
  --out sample_results.clean_projected
  --read-freq sample_results.clean.acount
  --score sample_results.clean.eigenvec.allele 2 5 header-read no-mean-imputation variance-standardize list-variants
  --score-col-nums 7-16

Start time: Mon Jul 15 08:34:33 2024
3836 MiB RAM detected, ~3175 available; reserving 1918 MiB for main workspace.
Using up to 8 compute threads.
504 samples (0 females, 0 males, 504 ambiguous; 504 founders) loaded from
sample_data.clean.fam.
1235116 variants loaded from sample_data.clean.bim.
Note: No phenotype data present.
--read-freq: PLINK 2 --freq file detected.
--read-freq: Frequencies for 324375 variants loaded.
Calculating allele frequencies... done.

Warning: 648750 --score file entries were skipped due to mismatching allele
codes.
Error: No valid variants in --score file.

End time: Mon Jul 15 08:34:34 2024

[Christopher Chang]

Ok, I need to update the online documentation to address the PROVISIONAL_REF? column that may now be in the --pca output; sorry about that.  I expect the command to work after you change "2 5" to "2 6".

[luca sclisizzo]

This is the partial output of .acounts file generated by --pca:

#CHROM  ID      REF     ALT     PROVISIONAL_REF?        ALT_CTS OBS_CT
1       1:14930:A:G     A       G       Y       415     1004
1       1:15774:G:A     G       A       Y       28      1002
1       1:15777:A:G     A       G       Y       74      1002
1       1:57292:C:T     C       T       Y       105     996
1       1:77874:G:A     G       A       Y       20      1002
1       1:87360:C:T     C       T       Y       23      1006
1       1:92917:T:A     T       A       Y       3       994
1       1:104186:T:C    T       C       Y       502     1002
1       1:125271:C:T    C       T       Y       973     1004
1       1:232449:G:A    G       A       Y       185     1004
1       1:533113:A:G    A       G       Y       131     1000
1       1:565697:A:G    A       G       Y       337     1004
1       1:566933:A:G    A       G       Y       14      1000
1       1:567092:T:C    T       C       Y       11      1000
1       1:568024:A:G    A       G       Y       17      992
1       1:569602:G:A    G       A       Y       34      1002
1       1:625392:T:C    T       C       Y       22      1006
1       1:705397:T:C    T       C       Y       12      1004
1       1:714031:G:A    G       A       Y       2       1004
1       1:716131:C:T    C       T       Y       21      998

What do you suggest?

[luca sclisizzo]

Changing the columns to 2-6 all goes in the correct direction. Why is it important to add also the ALT_CTS column?

Thank you!