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picard MarkDuplicates I=/scratch_tmp/prj/precision/lpwgs_bam/duke/bam_mdup1/20601_DCIS.md.bam OUTPUT=/scratch_tmp/prj/precision/lpwgs_bam/duke/test/20601_DCIS.md.bam METRICS_FILE=/scratch_tmp/prj/precision/lpwgs_bam/duke/test/20601_DCIS.md_metric.txt REMOVE_DUPLICATES=true

# Generate recalibration table with GATK BaseRecalibrator
gatk BaseRecalibrator -I ./test/20601_DCIS.md_qmap.bam \
    -R /scratch_tmp/prj/precision/lpwgs_bam/duke/Homo_sapiens_assembly38.fasta \
    --known-sites /scratch_tmp/prj/precision/lpwgs_bam/duke/Homo_sapiens_assembly38.dbsnp138.vcf.gz \
    --known-sites /scratch_tmp/prj/precision/lpwgs_bam/duke//Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
    -O /scratch_tmp/prj/precision/lpwgs_bam/duke/test_calibrated/recal_data.table

# Apply the recalibration table
gatk ApplyBQSR -I ./test/20601_DCIS.md_qmap.bam \
    -R /scratch_tmp/prj/precision/lpwgs_bam/duke/Homo_sapiens_assembly38.fasta \
    --bqsr-recal-file /scratch_tmp/prj/precision/lpwgs_bam/duke/test_calibrated/recal_data.table \
    -O /scratch_tmp/prj/precision/lpwgs_bam/duke/test_calibrated/20601_DCIS.md_qmap_recalibrated.bam