This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Downloading a Small VCF File

For my RNA-Seq project, I need a very small vcf file. I just need to use it for testing so it just has to be correctly formatted with minimal information. I was looking at the 1000 genomes project website and came up with this link: http://www.1000genomes.org/ftpsearch and I specified my search to vcf files but there are just too many to look through and attempt to download. Does anyone know of a good download from the link provided or an entirely new download I could use?

rna-seq
• 13,663 views • link
updated by Ram Ram • written by thorwahl • thorwahl

1 answer

If you search for trio*vcf and scroll down a little, you get to this file:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/trio/snps/trio.2010_06.ychr.sites.vcf.gz

It's 50KB, so nothing that will stress out your hardware, and you can always open it in an editor and lop off lines at the bottom. It's also got the benefit that it lists information for only a few genomes, not the proverbial 1000, so the lines are narrow enough to fit on a screen. That was my motivation to search "trio".

• 0 views • link
updated by Ram Ram • written by eric.kern13 eric.kern13

Log in to answer this question.

More posts like this