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. 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)?
AFAIK you can incorporate such info in the variant calling step with GATK's
Variant Recalibration 'known variants' option. Not sure if you can take variants into effect at during assembly.
EDIT: I meant to tell you of the "known variants" option available with GATK, not the Variant Recalibrator. I apologize for the confusion.
Maybe this is what you are looking for: http://www.bioconductor.org/packages/release/bioc/html/FunciSNP.html