Looking for a deletion in 1000 genomes

Question

[eyb]

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?

Answer 1

[Ram]

On the VCF file for chr1 from 1000 genomes, since you already know the gene as well as the population, why not just do the following:

1. GATK's SelectVariants to pick only the genotypes corresponding to your population (you can get the genotype to population info from the 1000 genomes website - I can help you get there if you wanna do this)
2. vcftools with --chr, --start and --end to pick the gene region

That should give you a manageable region that you could use UNIX utils with, even eyeball.

Or, you could zoom in to the region on the UCSC genome browser, enable 1000 genomes track in full mode and gain a visual perspective on it.

Also, 1000 genomes has VCF files per chromosome. Maybe you ran the CNV extractor on the wrong file?

[eyb]

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.