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  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/e3ca994eed65b55cce0b449422c38e/.command.sh
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/e3ca994eed65b55cce0b449422c38e/.command.run
==> STAGING COMPLETE (19 inputs)

INFO: Loading models...
INFO: Reading VCF: germline_control_2.entropy.vcf.gz
INFO: Loaded 394 variants (369 SNVs, 25 INDELs)
INFO:   INDEL entropy: 23 present, 2 missing (using -1 sentinel)
INFO: Annotating with BED files...
INFO:   Blacklist hits: 8
INFO:   Low depth hits: 0
INFO:   Boosted exon hits: 90
INFO:   SNV FP region hits: 30
INFO:   INDEL FP region hits: 9
INFO:   INDEL FP rate lookups (TSV): 15241 variant keys loaded
INFO:   RepeatMasker hits: 30
INFO: Applying models...
INFO: Results: 354 PASS (336 SNV, 18 INDEL), 40 RF_FAIL
INFO: Writing output VCF: germline_control_2.haplotyper_rf.rf_filtered.vcf.gz
INFO: Done!