Hello,
Has anyone tried to overlay human genomes variants with the 1000G or Hapmap or dbsnp. If so, what are the results like ?
For my human genomes, I tried to overlay using vcftools-
1) the solid data ( 3.2 million SNPs) with Hapmap (ftp://ftp.broadinstitute.org/bundle/...p_3.3.hg19.vcf ) :This gives me approx 22% overlay
2) the same sample sequenced with illumina (4.1 million SNPs) with Hapmap gives me 23%
Similarly, with dbsnp I get 54% for solid and 63% with illumina.
I am not sure if these results look good or I'm going wrong somewhere with my analysis.
Thank you.
Has anyone tried to overlay human genomes variants with the 1000G or Hapmap or dbsnp. If so, what are the results like ?
For my human genomes, I tried to overlay using vcftools-
1) the solid data ( 3.2 million SNPs) with Hapmap (ftp://ftp.broadinstitute.org/bundle/...p_3.3.hg19.vcf ) :This gives me approx 22% overlay
2) the same sample sequenced with illumina (4.1 million SNPs) with Hapmap gives me 23%
Similarly, with dbsnp I get 54% for solid and 63% with illumina.
I am not sure if these results look good or I'm going wrong somewhere with my analysis.
Thank you.