Hello everyone,
I am doing exome analysis using hg19 and dbSNP138 (both with 'chr' notation) downloaded from GATK resource bundle. However, given the recent release of dbSNP141 we would like to start using it for the calling process (as sequences are almost all aligned and calibrated with dbSNP138) .
My question, sorry if it seems to obvious as I'm still novice in exome analysis, is whether the new dbSNP141 will work smoothly as it is downloaded or should I do several adjustments? I have noticed that dbSNP 141 downloaded from ncbi presents rs under 'nochr' nomenclature starting by chromosome1, whilst dbSNP 138 dowloaded from bundle (for hg19) presents rs under 'chr' nomenclature and starting by ChrM.
so I am guessing I should add 'Chr' to dbSNP 141, should I reorder it too so chrM is the first? any other recommendations wuld be highly appreciated!!
thanks!!
