UnifiedGenotyper --genotype_likelihoods_model INDEL --output_mode EMIT_ALL_CONFIDENT_SITES

vanheel123vanheel123 Posts: 5Member
edited January 2013 in Ask the GATK team

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

Post edited by Geraldine_VdAuwera on

Comments

  • ebanksebanks Broad InstitutePosts: 687Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin

    Hi David,

    Yes, EMIT_ALL_SITES and EMIT_ALL_CONFIDENT_SITES are not intended to be used with the INDEL model.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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