PHVG v2.3.2 Patch Release
This patch release updates the Mercury workflows and adds a new output variable ivar_variant_proportion_intermediate
Mercury patches
This release adds the "covv_consortium" column to the output GISAID metadata file in the Mercury workflows. This new optional column has been added to the metadata formatters, which can be found here: Mercury_PE/_SE_Prep at gs://theiagen-public-files/terra/mercury-files/Terra_Metadata_Formatter_2023_05_22.xlsx, and Mercury_Prep_N_Batch at gs://theiagen-public-files/terra/mercury-files/Mercury_Prep_N_Batch_SC2_Metadata_Formatter_2023_05_22.xlsx.
Also, empty date values will now fail more informatively in Mercury_Prep_N_Batch.
New output variable
The variant_call task has been modified to now calculate the proportion of variants at intermediate allele frequencies (60-90%). This value is reported in the output column ivar_variant_proportion_intermediate for workflows that use iVar to perform variant calling (TheiaCoV_Illumina_PE and TheiaCoV_Illumina_SE).
What's Changed
- Update README.md by @kevinlibuit in #218
- Add "consortium" to Mercury_Prep by @sage-wright in #222
- Add intermediate frequency mutations screen TheiaCoV by @michellescribner in #220
- Mercury Fix when collection_date is missing by @sage-wright in #219
- update checksums by @sage-wright in #223
Full Changelog: v2.3.1...v2.3.2
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