Question: PLINK returns NA values for all minor allele frequencies in my data
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yorgos.athanasiadis • 40 wrote:
Hi,
I'm having the following problem with PLINK:
I am using the --freq command to calculate allele frequencies from an input that was created from 23andMe data. However all I get in the frq report is NA estimates for all minor allele frequencies:
CHR SNP A1 A2 MAF NCHROBS 1 rs12564807 0 A NA 0 1 rs3131972 A G NA 0 1 rs148828841 A C NA 0 1 rs12124819 G A NA 0 1 rs115093905 T G NA 0 1 rs11240777 A G NA 0 etc...
Same thing goes for --hwe etc. --missing is the only command that seems to be working, so I know that the file is read correctly.
I don't know what's wrong because PLINK reads the input files correctly. I suspect it is the allele coding, but I have tried several solutions and they still don't work. Has anyone come accross with a similar issue?
Yorgos
Can you post your log file.
Sure!
Try adding --nonfounders to the command line. Normally, PLINK --freq and --hwe excludes all samples with at least one parental ID; so if everyone in your dataset has parental IDs (it's necessary to use '0' to indicate an unknown parent), that would explain your result.
(You should also use the most recent build: there was a --nonfounders bug fixed on September 26th.)
If --nonfounders does not fix the problem, let me know.
I spent the entire morning testing different files and I got to the exact same conclusion:
When I first built the ped file, I assigned a non-zero father and mother to all my individuals, so there were no founder individuals left to be used for allele frequency calculations. I was just about to re-built the file with 0's for dads and mums, but then I saw your reply: --nonfounders flag actually worked, so thank you so much!
I don't know if I should lough or cry, ha ha ha...
Did you check your plink.hh file? It says you have a lot of haploid genotypes present. This suggests that your file format might be off.
I did check it and I tried different things to solve the problem (including using the --set-hh-missing option and by removing X, Y, XY and mtDNA SNPs), but the problem persists...
Any ideas? :-/