search

dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
145 stars 37 forks source link

improve handling of DeepVariant non-called gVCF records #195

Closed mlin closed 4 years ago

mlin commented 4 years ago

Compared to other callers, DeepVariant generates more non-called (./.) gVCF records to express uncertainty; including both reference bands and variant records. In 497277a we made sure to preserve the non-called status for reference bands, albeit in a heavy-handed way that censored all the QC fields (RNC=PartialData).

Here we introduce a new RNC InputNonCalled, used for both reference bands and variant records when applicable, which preserves the associated QC fields in the pVCF.

coveralls commented 4 years ago

Coverage Status

Coverage increased (+0.001%) to 93.401% when pulling e35d827c2f7af14be24f00ec30444713e93180a9 on mlin-dv-noncalled into ba6250fcc884a9c4013e3eff2b0739f0f45a23a4 on master.