Hi
I need to obtain SNPs and genotypes for 30 lymphoblastoid cell lines.
I had been told these 30 individuals (CEU and YRI) had all been genotyped as part of the 1000genomes project, however this turns out not to be true: in the last 1000genomes iteration I can only find .vcf files for 16 of my individuals. Some of the missing 14 appear to have been part of the project at some point, however there is no trace of them in the current dataset.
I have then looked in Omni 2.5 data, again part of the 1000genomes data. Here I find vcf for a total of 23 individuals, a superset of the 16 individuals I mentioned before.
So I'm still short of data for 7 individuals. I think hapmap should have data for these, but I'm not sure. Do I have any other alternatives? If hapmap is my only option, what is the best way to get .vcf files with genotypes from the hapmap project for these 7 individuals (and possibly for all 30 of them, for coherence reasons)?
Thank you in advance for your help!
I need to obtain SNPs and genotypes for 30 lymphoblastoid cell lines.
I had been told these 30 individuals (CEU and YRI) had all been genotyped as part of the 1000genomes project, however this turns out not to be true: in the last 1000genomes iteration I can only find .vcf files for 16 of my individuals. Some of the missing 14 appear to have been part of the project at some point, however there is no trace of them in the current dataset.
I have then looked in Omni 2.5 data, again part of the 1000genomes data. Here I find vcf for a total of 23 individuals, a superset of the 16 individuals I mentioned before.
So I'm still short of data for 7 individuals. I think hapmap should have data for these, but I'm not sure. Do I have any other alternatives? If hapmap is my only option, what is the best way to get .vcf files with genotypes from the hapmap project for these 7 individuals (and possibly for all 30 of them, for coherence reasons)?
Thank you in advance for your help!