Question

Saving file as .vcf

0

Entering edit mode

2.5 years ago

Maryam ▴ 10

Hello,

I really need help to save my file as .vcf.

I have modified my vcf file as I want using VCFR package in R. Now I want to save my new in .vcf format using code write.vcf.

But the saved file is some kind of weird data file. Can someone help me where I am making mistake?

Thank you enter image description here

NGS Variant VCF • 1.2k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 2.5 years ago by Maryam ▴ 10

0

Entering edit mode

from manual:

The function write.vcf takes an object of either class vcfR or chromR and writes the vcf data to a
vcf.gz file (gzipped text)

ADD REPLY • link 2.5 years ago by cpad0112 21k

score 2 · Answer 1 · 2022-05-16

2

Entering edit mode

2.5 years ago

ATpoint 85k

This gibberish means that it is probably gzip-compressed and should be vcf.gz. Please don't get used to open OMICS files in plain text editors. Use Unix tools such as less, head or something like that.

ADD COMMENT • link 2.5 years ago by ATpoint 85k

0

Entering edit mode

What I should do?

ADD REPLY • link 2.5 years ago by Maryam ▴ 10

0

Entering edit mode

Rename your file to .vcf.gz and then try and see whether something like zless can properly open it. Frankly, and I really mean no offense, if you are stuck with these kinds of basics you must spend time with Unix fundamentals before diving into analysis.

ADD REPLY • link 2.5 years ago by ATpoint 85k

0

Entering edit mode

Thank you so much. I just uncompressed my files.

ADD REPLY • link 2.5 years ago by Maryam ▴ 10

0

Entering edit mode

Why did you delete the post?

ADD REPLY • link 2.5 years ago by Ram 44k