Dear Community,
I am trying to construct an individual genome from reference genome in fasta format and his/her structure variation file in VCF format. I downloaded the VCF file from 1000 genome project page and the reference from the UCSC genome browser.
The basic idea is to delete the corresponding region when the VCF tells me there is a deletion in that region and insert some sequence when there is an insertion, and here comes my question. In the VCF file provided by the 1000 genome project, it stated that if the SVTYPE=ALU/SVA/LINE1, it would mean insertion of either ALU, SVA, or LINE1 elements.
So it is natural for me to google like where can I download human ALU elements? However, I could not find the link or location to download all these files.
Also, after browsing through the vcf file, I found that some alu elements are called aluUndef, any idea of what that is ?
