Extract specific variants from vcf to annotate

Question

[arwa.ahmad95]

Hi

I have a txt file that contains some variants with specific columns

Example from my txt file

chr5    140673  rs12516245  A   G

I want to extract variants that in txt from a large VCF file to a new VCF file. So a new VCF file just contain this variants with the header to annotate a new VCF file in the final step. How can I do this please?

I'm new in bioinformatics, please help me

[Ram]

Did you Google "extract from VCF" or "subset from VCF"? You may be new to bioinformatics but you must have tried something before posting here.

[arwa.ahmad95]

yes, I try to google it but I didn't find the answer ( I found how to subset samples or region for example ) but I didn't found how to subset like what I really need!

[Ram]

I found how to subset samples or region for example

You have then found the solution - your text file has the region information and you can use what you found to extract records overlapping those regions.