This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Uncompress The 1001 Genome vcf.gz

Hi everybody. Is there any Linux command to uncompress .vcf.gz format. I ma using windows winrar at the moment but it's too slow. Many thanks.

vcf
• 8,744 views • link
updated by Petr Ponomarenko Petr Ponomarenko • written by sarah.k • sarah.k

What would you do knowing linux command, if you are using windows? What are you planning to do with the file? You may not need to uncompress it.

• 0 views • link
written by GenoMax GenoMax

I want to import it to a NoSQL database such as Apache Cassandra on my Linux machine. But I can't find a way to uncompress it. So, I've decided to uncompress it in windows then move the .vcf file on my Linux machine.

• 0 views • link
written by sarah.k • sarah.k

I want to import it to a NoSQL database such as Apache Cassandra on my Linux machine.

curious ; why ?

But I can't find a way to uncompress it

why don't you move the *.vcf.gz on linux before uncompressing it with gunzip ?

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

for your first question: looking for new database generation for restore and retrieval genomic data and its data modeling. for your second question: I have my data on Linux machine too. what is gunzip? Do you have an example of using it to decompress .vcf.gz file?

• 0 views • link
written by sarah.k • sarah.k

I've also used your vcf2sql script. But it didn't work for my data.

• 0 views • link
written by sarah.k • sarah.k

it didn't work for my data

Without the command used, the exact error message, and / or a sample of the data, no one can possibly help you.

• 0 views • link
written by h.mon h.mon

which dataset do you use? There are many vcf files. I do not know which one is used for gwas analysis. Thanks.

• 0 views • link
written by shawn • shawn

1 answer

gunzip

most commands in linux have gzip compressed file support versions. For example zcat, zmore, zgrep... Most bioinformatics tools support gzip-compressed files, for example: vcftools --gzvcf your.vcf.gz

• 0 views • link
written by Petr Ponomarenko Petr Ponomarenko

Log in to answer this question.

More posts like this