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Hi,

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.

thanks,

david van heel

There are 1 comments on this article. To see them or add your own, view this post on the forum