Does anyone know what reference data they used for alignement in phase 3, 20130502 release?
Browsing through their ftp I have only found phase 2 reference (ftp://ftp.1000genomes.ebi.ac.uk/vol1...cal/reference/). There are some fasta reference files dated 2013 (same time as release), but I am not sure if they are what I am looking for. In my understanding they have applied bwa to aling released data in phase 3, but reference has cg in its name.
It is weird because data is there, but It is unclear what reference to use with them.
Thanks
Browsing through their ftp I have only found phase 2 reference (ftp://ftp.1000genomes.ebi.ac.uk/vol1...cal/reference/). There are some fasta reference files dated 2013 (same time as release), but I am not sure if they are what I am looking for. In my understanding they have applied bwa to aling released data in phase 3, but reference has cg in its name.
It is weird because data is there, but It is unclear what reference to use with them.
Thanks
