The 1000 Genomes FTP site under goes periodic rearrangments to accomodate new data sets coming in and to preserve old data in a new location.
If there is a particular file where you don't know if it still exists, the best place to try is our current.tree file.
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree
This file contains five columns:
- relative path
- type (directory or file)
- size in bytes
- last updated time stamp
- md5
You should be able to search this file with your filename and see if the file still exists and find its new location.
If you still can't find your file email info@1000genomes.org and the support team will be able to tell you what has happened to it.