vcf.gz to vcf

Question

[sooni]

Hello. I want to unzip 'vcf.gz' file.

bgzip -d my.vcf.gz

In Linux, when I run the above code, I get the following error:

[bgzip] my.vcf.gz: not a compressed file -- ignored

How can I solve this problem?

Answer 1

[Mark]

As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named my.vcf.txt yet be compressed.

Use the file command to get file type in linux:

% echo test > my.vcf.gz
% file my.vcf.gz
my.vcf.gz: ASCII text

Let's fix this by changing the extension:

% mv my.vcf.gz my.vcf
% gunzip my.vcf
% file my.vcf.gz
my.vcf.gz: gzip compressed data, was "my.vcf"...

However or whatever generated that vcf file did not output a compressed vcf.gz file.

[Brian Bushnell]

Nice solution! Normally I run "head" on it which ruins my Putty instance.

[Mark]

!! The same happens to me when I accidentally do this! I never found a way to recover the instance. I think There's some escaped characters that terminals the garbled strings returning the instance to normal characters. Similar to output colors to the terminal eg \033[0m to end color.