Question: Uncompress The 1001 Genome vcf.gz
0
gravatar for sarah.k
2.5 years 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 • 2.6k views
ADD COMMENTlink modified 2.5 years ago by Petr Ponomarenko2.6k • written 2.5 years 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 2.5 years ago • written 2.5 years ago by genomax74k

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 2.5 years 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 2.5 years ago by Pierre Lindenbaum124k

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 2.5 years ago by sarah.k0
2

what is gunzip?

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

gunzip file.vcf.gz
ADD REPLYlink written 2.5 years ago by Pierre Lindenbaum124k

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

ADD REPLYlink written 2.5 years 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 2.5 years ago by h.mon28k

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 9 months ago by shawn20
3
gravatar for Petr Ponomarenko
2.5 years 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 2.5 years ago • written 2.5 years ago by Petr Ponomarenko2.6k
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