As an additional caveat, we should mention that Pascal uses the European 1KG sample as reference population per default. This choice may not be appropriate if the studied sample is not of European origin. In this case the user is encouraged to supply Pascal with the appropriate reference panel. Also, SNPs with low MAF are by default excluded from the analysis, because the low number of individuals in the European 1KG sample limits the accuracy of the LD estimate for low frequency variants. If the user wishes to include lower frequency variants, the use of a reference sample containing more individuals is recommended.
