I had a list of interesting SNPs from tumor samples, I am wondering how I can remove the SNP associated with population identified through HapMap or 1000 Genomes. I would like to pick one of the following two ways:
1) filter dbSNP131 and 1000 Genome using annovar;
2) filter dbSNP or 1000 Genome SNPs using BedTools to filter UCSC dbSNP 137.
After filtering, almost nothing left, the left SNPs should be high-confidence, right?
Thanks!
1) filter dbSNP131 and 1000 Genome using annovar;
2) filter dbSNP or 1000 Genome SNPs using BedTools to filter UCSC dbSNP 137.
After filtering, almost nothing left, the left SNPs should be high-confidence, right?
Thanks!