I have been trying to prepare a SNP file for my NGS analysis. Basically the file should have following information, rsId, chromosome, position, allele, allele freq, counts, population, minor alleles and MAF. And the information should be based on hg 19 (build 37.3) and should have the population information.
HapMap releases (rel 28 & 27) has based on NCBI build 36 and dbSNP b126. And moreover, BioMart-Martview allows only rel 27 retrieval. If i want to use rel 28, ll have to parse the data from ftp site and create one of my own.
1000 Genome project says "The 1000 genomes snp and short indel all get submitted to dbSNP and are available from version 132".
Latest release of dbSNP (135) has 1000 Genome data annotated to it with population information.
So now if i want to have the latest SNP information that i have mentioned above which database should i go for?