Question: Genotype input in matrix eqtl with dosage dataset
1
gravatar for Molly_K
8 months ago by
Molly_K60
United States
Molly_K60 wrote:

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!

eqtl genotype dosage • 288 views
ADD COMMENTlink modified 8 months ago by devidjohn470 • written 8 months ago by Molly_K60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 902 users visited in the last hour