profile scoring output columns

[Hamel Patel]

Hi,

I have created a profile score using PLINK2, and am confused to what the columns CNT and CNT2 represent.

Here is a snapshot of my output:

         FID          IID         PHENO    CNT   CNT2    SCORE
  sample_01   sample_01     -9         34      6          -0.00694594
  sample_02   sample_02      1         48      6          -0.00962895
  sample_03   sample_03     -9         36      6          -0.0057536
  sample_04   sample_04     -9         52      6           0.00534785

According to the PLINK website:

CNT  -Number of non-missing SNPs used for scoring
CNT2 -The number of named alleles

I have only used 35 SNPs to calculate the scores, so how can CNT column be higher than 35?

What do you mean by named alleles?

And are the CNT and CNT2 column contents possibly swapped?


Thanks,
Hamel.

[Christopher Chang]

Does PLINK 1.07 give the same results?  If not, there may be a bug in 1.9; if you could send me a small fileset to reproduce the bug with, that would be helpful.

[Christopher Chang]

With that said, looking at the plink2 file format documentation, I don't think there's a bug:

https://www.cog-genomics.org/plink2/formats#profile

CNT	Number of nonmissing alleles used for scoring
CNT2	Sum of named allele counts

Assuming your SNPs are all diploid, CNT is *twice* the number of SNPs used, because each SNP call involves two alleles.  And CNT2 is the number of allele calls which match those in the score file.  E.g. 52/6 means 26 SNPs were present, and 6 out of the 52 allele calls match named alleles in the score file.

[Hamel Patel]

Thanks for the clarification Christopher!

[ep...@bristol.ac.uk]

Hi,

Related to the post below. 

In the log file when --score what does "number mapped to SNPs; number to alleles" mean and why are they different?

Thanks.

Evie

[Christopher Chang]

In PLINK 1.07, "number mapped to SNPs" reports the number of entries in the score file which correspond to loaded variant IDs, and "[number mapped] to alleles" reports the number for which the named allele was also valid.