Genotyping variants from BAM (human)

Question

[German.M.Demidov]

Hi, I have a list of rs-ids and I would like to genotype several thousand of WGS (BAMs) without performing actual calling and VCF file generation.

What would be the best tool for this task?

(I can convert rs-ids to VCF or bed, not a problem, but which tool can be used for genotyping?)

[GenoMax]

without performing actual calling and VCF file generation

So basically get a count of bases at a particular position? igvtools or perbase (LINK).

[German.M.Demidov]

Thanks a lot! I think there are no indels in this list, but what if there is an indel?

[GenoMax]

Then there is a problem. On a serious note, indels are always going to cause problems with location based stats.