<p>I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs.
I am trying to test with chromosome 5 as I have both bgen and sample file. I am using plink 2 for the conversion of bgen and sample file<br />
<code>plink2 --bgen ukb_chr5_v3.bgen ref-first --sample ukb22828_c5_b0_v3_s487239.sample --make-bed --out testfile</code></p>
<p>I am getting three files as output like .pgen .psam .pvar.
This is how .psam looks like,</p>
<div class="s-table-container">
<table class="s-table">
<thead>
<tr>
<th style="text-align: left;">FID</th>
<th style="text-align: center;">IID</th>
<th style="text-align: right;">sex</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left;">482828</td>
<td style="text-align: center;">482282</td>
<td style="text-align: right;">1</td>
</tr>
</tbody>
</table>
</div>
<p>and .pvar file has five columns, chromosome, position, ID, ref allele, alt allele.
I am still confused which IDs have the corresponding alleles/genotypes.
Please guide me in further analysis. My goal is find genetic data of specfic IDs which I am looking for.
Thanks</p>

CC BY-SA 4.0
2021-10-28T10:15:50.920Z
The genotypes are in the ``.pgen`` file, but encoded as a binary, so you can't query it directly. What are you going to do with the genotypes?
user438383
CC BY-SA 4.0
2021-10-28T12:33:48.557Z
My aim is to calculate polygenic risk scores using pre-calculated weights for each individual and for that I possibly need effect allele count (0,1, or 2)
Muhammad
<r><plink><phylogenetics><epidemiology>
Linking UK biobank patient IDs with their corresponding genetic data
# Linking UK biobank patient IDs with their corresponding genetic data

(Asked by: username_0 on 2021-10-27)

I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs.
I am trying to test with chromosome 5 as I have both bgen and sample file. I am using plink 2 for the conversion of bgen and sample file  
`plink2 --bgen ukb_chr5_v3.bgen ref-first --sample ukb22828_c5_b0_v3_s487239.sample --make-bed --out testfile`

I am getting three files as output like .pgen .psam .pvar.
This is how .psam looks like,

| FID | IID | sex |
| --- | --- | --- |
| 482828 | 482282 | 1 |

and .pvar file has five columns, chromosome, position, ID, ref allele, alt allele.
I am still confused which IDs have the corresponding alleles/genotypes.
Please guide me in further analysis. My goal is find genetic data of specfic IDs which I am looking for.
Thanks

**Tags:** r, plink, phylogenetics, epidemiology
> **Comments:**
> **username_1**: The genotypes are in the ``.pgen`` file, but encoded as a binary, so you can't query it directly. What are you going to do with the genotypes?  
> **username_0**: My aim is to calculate polygenic risk scores using pre-calculated weights for each individual and for that I possibly need effect allele count (0,1, or 2)  

---

## 0 answers

