Question: Easiest way to determine copy number for all SVs in all samples in 1000 Genomes
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gravatar for Ryan D
5.3 years ago by
Ryan D3.3k
USA
Ryan D3.3k wrote:

Hello Biostars,

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.

Thanks,

Rx

ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 5.3 years ago by Ryan D3.3k

Not an answer to the question, but ostensibly the most recent phase3 release does have copy number declarations in it:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ . That information comes from Laura Clarke with the 1000 Genomes Project.

Ryan

ADD REPLYlink written 5.3 years ago by Ryan D3.3k
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