I was wondering if there is a PLINK file available that has the copy number status of all structural variants (SVs) for samples in the 1000 Genomes. I know they are often named with names such as MERGED_DEL_2_106009 which is the same as esv2666691 in the UCSC genome browser. What I wanted to know is either A) if the file (or one like it) already exists or B) if not, what would be the easiest way to generate such a file. Ideally we would have a file that has the sample name on each line and each column would have a 0,1, or 2 for the copy number state for each SV.
I can pull them one at a time and I imagine there is a way to use tabix to get all SVs for a chromosome for all 1000 Genomes samples and then combine VCF files, but wonder if we could do this for all SVs in the genome at once.
Seems like something I should know, but do not. So I appreciate any help. There are apparently calls available in the current release.