I have performed eQTL with matrix eQTL tool before with hard call genotype. I wonder if anyone has tried with dosage genotype. The data format is
SNP A1 A2 F1 I1 F2 I2 F3 I3 rs0001 A C 0.98 0.02 1.00 0.00 0.00 0.01 rs0002 G A 0.00 1.00 0.00 0.00 0.99 0.01
Can I just use this file as input? F1 I1 are usually using the same ID, so the file looks like
SNP A1 A2 ID01 ID01 ID02 ID02 ID03 ID03 rs0001 A C 0.98 0.02 1.00 0.00 0.00 0.01 rs0002 G A 0.00 1.00 0.00 0.00 0.99 0.01
Can matrix eQTL identify the matching individual? or I need a different genoytpe format, if so, what kind? Thank you!