Genotyping variants from BAM (human)
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10 weeks ago

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?)

genotyping • 226 views
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without performing actual calling and VCF file generation

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

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

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

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