I'm running DeepVariant Pepper on various samples from different trios. I need to carry out joint genotyping as I need to be aware of when a variant is homozygous reference and when there is poor confidence in a region so the variant couldn't be determined.
I'm running DeepVariant Pepper on various samples from different trios. I need to carry out joint genotyping as I need to be aware of when a variant is homozygous reference and when there is poor confidence in a region so the variant couldn't be determined.
I've tried using GLNexus but there appears to be an issue with the format of the gVCF from pepper - see issue https://github.com/dnanexus-rnd/GLnexus/issues/287
Are there any recommendations for different joint genotyping approaches?
Thanks!
Sophie