1000 Genome Project Structural Variants for Illumina

Question

[Yasin Uzun]

I am trying to access 1000 Genome Project structural variants (SV). I specifically need the variants called on Illumina sequenced samples. In the read me file (http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/README_phase3_sv_callset_20150224) in here https://www.internationalgenome.org/phase-3-structural-variant-dataset/ I found out that CGI SVs are in these links.

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/cgi_variant_calls/filtered_calls/ALL.wgs.cgi_from_um.20131022.deletions.genotypes.fullFilter.vcf.gz

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/cgi_variant_calls/filtered_calls/ALL.wgs.cgi_from_um.20131022.duplications.genotypes.fullFilter.vcf.gz

But I could not find SVs called for Illumina sequenced samples. There are SV calls in these directories: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/supporting/GRCh38_positions/

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/input_callsets/

But in the README files, I can't see they are based on Illumina data or not. Can I assume that unless specified otherwise, all the SV calls in these directories are based on Illumina data?

In addition, in the second link I can see that SVs are lifted to GRVh38, are all the remaning ones GRCh37? May I assume that all the coordinates are GRCh37, unless specified otherwise?

Does anybody know about it? Thanks!

Answer 1

[trausch]

These SV calls are based on illumina data and GRCh37:

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/

The GRCh38 subdirectory are the lifted SV calls.