dosage file format

[YEDA WU]

To whom it may concern,

I am new to PrediXcan. The dosage file format for PrediXcan is as follows:

Columns are

 chromosome rsid position allele1 allele2 MAF id1 ..... idn.

I am wondering if I only have PLINK bfiles, how can I convert that to the dosage file format for PrediXcan?

Also, "dosage for each person refers to the number of alleles for the 2nd allele listed (between 0 and 2)", does it mean the allele count in dosage file is generated according to A2?

Thank you in advance.

Y

[Alvaro Barbeira]

Hi Yeda,

There is a script in the PrediXcan repository to convert PLINK files to PrediXcan format: https://github.com/hakyimlab/PrediXcan/blob/master/Software/convert_plink_to_dosage.py

And yes, the second allele is used for the count, and is interpreted as "effect allele".

Hope this helps. Best,

Alvaro

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[YEDA WU]

Thank you very much!

在 2018年3月14日星期三 UTC+10下午11:51:22，Alvaro Barbeira写道：

Hi Yeda,

There is a script in the PrediXcan repository to convert PLINK files to PrediXcan format: https://github.com/hakyimlab/PrediXcan/blob/master/Software/convert_plink_to_dosage.py

And yes, the second allele is used for the count, and is interpreted as "effect allele".

Hope this helps. Best,

Alvaro

On Wed, Mar 14, 2018 at 4:45 AM, YEDA WU <wuyed...@gmail.com> wrote:

To whom it may concern,

I am new to PrediXcan. The dosage file format for PrediXcan is as follows:

Columns are

 chromosome rsid position allele1 allele2 MAF id1 ..... idn.

I am wondering if I only have PLINK bfiles, how can I convert that to the dosage file format for PrediXcan?

Also, "dosage for each person refers to the number of alleles for the 2nd allele listed (between 0 and 2)", does it mean the allele count in dosage file is generated according to A2?

Thank you in advance.

Y

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