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Is there similar functionality as EMIT_ALL_SITES for Indels?
I noticed that you can use emit_all_sites in UnifiedGenotyper to gather information on alternate alleles at every base provided in the interval file. Is there a way to do this same process but with indels? I want to pass in an interval list of indel locations and a bam file and for every site in the interval list get number of reads supporting the indel and number of reference.