I have txt file which contains the chromosomal positions of interest:

chromPos.txt
1 55
1 56
1 58
1 67
1 69

and so on.

i would like to use it to filter my snpeff file. To achieve this, i use the following command:

bcftools view -R chromPos.txt -o regions.txt file.vcf.snpeff 

Since my input is a txt file, I get an error that bcfools is not able to parse the input file. My guess is that it arises due to the chromPos.txt format. I found threads concerning the same topic Best way to query VCF for specific variants My issue lies in the fact that I dont know how to make my text file a vcf file. Is it possible for a vcf file to only contain 2 columns (chrom and position)? I've tried mv chromPos.txt chromPos.vcf .It yields the same error as the txt file.

I am thankful for any advice you have for me.

Edit/Update: was able to solve all my issues regarding filtering and subsettinng the vcf file through the articles found at:

https://www.biocomputix.com/post/bcftools Highly recommend!