I am trying to convert plink files to VCF by using following commands

```
#!/bin/sh
# 1. have plink binary to specify reference allele
plink --noweb --bfile $plink_file --reference-allele $ref_Allele_file --make-bed --out $plink_file_modified

# 2. create plinkseq project
pseq $pseq_project new-project

#3. load plink file into plink/seq
pseq $pseq_project load-plink --file $plink_file_modified --id $plink_file_modified

#4. write out vcf file
pseq $pseq_project write-vcf | gzip > $plink_file_modified.vcf.gz
```

I have site-positions-file which looks like as follows

```
7    7672918
7    4458845
7    3013804
7    4518570
7    7216328
7    7523768
```

I need reference-allele-file like this

```
7    7672918   C
7    4458845   C
7    3013804   T
7    4518570   T
7    7216328   C
7    7523768   C
```

Kindly help me
<p>There are several older threads on this, like</p>

<p>https://www.biostars.org/p/47561/</p>

<p>or</p>

<p>https://www.biostars.org/p/5862/</p>

<p>I guess the easiest way to circumvent your few steps and the use of pseq is to just download the <a href="https://www.cog-genomics.org/plink2">PLINK 1.9</a> beta and use the <a href="https://www.cog-genomics.org/plink2/data#recode">recode</a> function</p>

<pre>
plink --file your_ped_map_input --recode vcf</pre>
