Changes

Take your dosage, geno, and info output (.dose, .geno and .info or .mldose, .mlgeno, and .mlinfo depending on non-mle or mle manner you've used) and check if dosage is the number of AL1 copies or AL2 copies. Example is given below:  

Take your dosage, geno, and info output (.dose, .geno and .info or .mldose, .mlgeno, and .mlinfo depending on non-mle or mle manner you've used) and check if dosage is the number of AL1 copies or AL2 copies. Example is given below:  

> head -1 mldose/chr21.mldose | cut -f3 -d ' ' 1.962 > head -2 mlinfo/chr21.mlinfo SNP Al1 Al2 Freq1 MAF Quality Rsq rs885550 2 4 0.9840 0.0160 0.9682 0.0021 head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' ' 2/2  

  head -1 mldose/chr21.mldose | cut -f3 -d ' '  

 

  1.962  

  head -2 mlinfo/chr21.mlinfo  

  SNP Al1 Al2 Freq1 MAF Quality Rsq  

  rs885550 2 4 0.9840 0.0160 0.9682 0.0021  

  head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' '  

  2/2  

Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs.  

Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs.