Question: Uncompress The 1001 Genome vcf.gz
0
gravatar for sarah.k
22 months ago by
sarah.k0
sarah.k0 wrote:

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 • 1.5k views
ADD COMMENTlink modified 22 months ago by Petr Ponomarenko2.6k • written 22 months ago by sarah.k0

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.

ADD REPLYlink modified 22 months ago • written 22 months ago by genomax64k

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.

ADD REPLYlink written 22 months ago by sarah.k0

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 ?

ADD REPLYlink written 22 months ago by Pierre Lindenbaum118k

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?

ADD REPLYlink written 22 months ago by sarah.k0
2

what is gunzip?

https://linux.die.net/man/1/gzip

gunzip file.vcf.gz
ADD REPLYlink written 22 months ago by Pierre Lindenbaum118k

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

ADD REPLYlink written 22 months ago by sarah.k0
1

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.

ADD REPLYlink written 22 months ago by h.mon24k

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

ADD REPLYlink written 5 weeks ago by shawn20
3
gravatar for Petr Ponomarenko
22 months ago by
United States / Los Angeles / ALAPY.com
Petr Ponomarenko2.6k wrote:

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

ADD COMMENTlink modified 22 months ago • written 22 months ago by Petr Ponomarenko2.6k
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