Fixed deprecated argument in GnarlyGenotyper.

Author: jonn-smith

wdl/tasks/VariantCalling/SRJointGenotypingPopulationScale.wdl

@@ -515,7 +515,7 @@ task GnarlyGenotypeGVCFs {
                 -L ~{interval_list} \
                 ~{dbsnp_vcf_arg} \
                 --merge-input-intervals \
-                --only-output-calls-starting-in-intervals \
+                --variant-output-filtering STARTS_IN \
                 --heterozygosity ~{heterozygosity} \
                 --heterozygosity-stdev ~{heterozygosity_stdev} \
                 --indel-heterozygosity ~{indel_heterozygosity} \