Genotype input in matrix eqtl with dosage dataset
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3.0 years ago
Molly_K ▴ 60

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!

dosage genotype eqtl • 1.1k views