Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/e434ad49a66b04e3816c3b0cfed0d5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4c0d18e23be13f7dcb703b2a8d5b5e/659_bTo-N1-BDNA-1_B23KFG5LT4_1.haplotyper_rf.rf_filtered.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/gt_correction_model_v2.joblib
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/e434ad49a66b04e3816c3b0cfed0d5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4c0d18e23be13f7dcb703b2a8d5b5e/659_bTo-N1-BDNA-1_B23KFG5LT4_1.haplotyper_rf.rf_filtered.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz
==> STAGING COMPLETE (7 inputs)

INFO: Loading GT correction model: gt_correction_model_v2.joblib
INFO: GT correction threshold: 0.5
INFO: Reading VCF: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.haplotyper_rf.rf_filtered.vcf.gz
INFO: Total variants: 31092, PASS INDELs to evaluate: 1370
INFO: Annotating PASS INDELs with Simple_repeat...
INFO:   Simple_repeat hits: 215
INFO: Predicting genotypes...
INFO: Writing output VCF: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.haplotyper_rf.gt_corrected.vcf.gz
INFO: GT corrections applied:
INFO:   Het -> Hom: 89
INFO:   Hom -> Het: 4
INFO:   Unchanged:  1277
INFO: Done!