I am looking to detect if there is GSTM1 deletion in CEU population from 1000 genome project. Can anyone advice where to start? I have tried to extract CNVs from 1000 genome vcf file using vcftools but it outputted only 5 deletions none of which were on chromosome 1. I was thinking about downloading sequence files but I am not sure what to download? Can anyone advice?
Thanks for advice. I've downloaded newest data for 1st chromosome separately and extracted indels using vcftools, though it was not helpful, since I am looking for ~15kb deletions, longest deletion there is ~100b. I think I will try to extract the region from 1000 genome sequence files.