When I use UnifiedGenotyper with --genotype_likelihoods_model SNP --output_mode EMIT_ALL_CONFIDENT_SITES I get the reference SNP homozygote calls (or ./. if insufficient depth/quality etc). Great!
But when I use UnifiedGenotyper with --genotype_likelihoods_model INDEL --output_mode EMIT_ALL_CONFIDENT_SITES I only get non-reference calls, everything else (i.e. reference homozygotes, and anything uncallable) is ./.
I want to be able to select variants (SNPs and INDELs) on call rate across samples - as one would do for array genotype data. And avoid case-control bias due to differential missingness.
david van heel