Plink --score generates different output for same dataset

Question

[ian15brown]

Hi, I am a newbie to plink2 and trying to generate scores on individuals. I happen to run plink2 multiple times on the same individuals genotyping data to get different scores. I am perplexed and not sure what I could be doing wrong.

Version:

PLINK v2.00a2LM 64-bit Intel (26 Aug 2019)

Command:

plink2 --score P-out-all.txt 2 4 6 'header' cols=+scoresums --pgen P.bed --pvar P.bim --psam P.fam --read-freq all.afreq

Multiple outputs on same data:

#FID IID NMISS_ALLELE_CT NAMED_ALLELE_DOSAGE_SUM SCORE1_AVG SCORE1_SUM
0 P_0001 19618 7856 -9.0482e-06 -0.177508
0 P_0001 19618 7856 -7.828e-06
0 P_0001 19618 7856 -8.64096e-06
0 P_0001 19618 7856 -8.06365e-06 -0.158193

Thanks for help.

Regards, Ian

[chrchang523]

This is being addressed at https://groups.google.com/forum/#!topic/plink2-users/5sbfhUoj2ms .