calling 1000G SNPs/indels from ngs data (chipseq or other source)

I would like to call known (e.g. from 1000G project) SNPs and indels from sequence reads, in my case a chip-seq project with 20 samples, which i will later also use to query allelic imbalance. Is there an easy way to call known SNPs/Indels ? (How) should i take into account the Indels/SNPs during allignment (because an indel is could be quite different from the reference genome)?