Genotyping variants from BAM (human)
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?)
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German.M.Demidov
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So basically get a count of bases at a particular position?
igvtoolsorperbase(LINK).Thanks a lot! I think there are no indels in this list, but what if there is an indel?
Then there is a problem. On a serious note, indels are always going to cause problems with location based stats.