Remove deprecated --genomicsdb-use-vcf-codec option.

See #3263 for discussion. Thanks to @amizeranschi for the heads up.

HISTORY.md

@@ -1,4 +1,5 @@
 ## 1.2.4 (in progress)
+- Remove deprecated `--genomicsdb-use-vcf-codec` option as this is now the default.
 - Add bismark output to MultiQC.
 - Fix PS genotype field from octopus to have the correct type.
 - Edit VarDict headers to report VCFv4.2, since htsjdk does not fully support VCFv4.3 yet.

bcbio/variation/gatkjoint.py

@@ -101,7 +101,6 @@ def _run_genotype_gvcfs_genomicsdb(genomics_db, region, out_file, data):
             params = ["-T", "GenotypeGVCFs",
                       "--variant", "gendb://%s" % genomics_db,
                       "-R", dd.get_ref_file(data),
-                      "--genomicsdb-use-vcf-codec",
                       "--output", tx_out_file,
                       "-L", bamprep.region_to_gatk(region)]
             params += ["-ploidy", str(ploidy.get_ploidy([data], region))]